![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15396 closed defect (fixed)
"Demoted" StructureSeq does not save/restore correctly
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.8 |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3-arm64-arm-64bit
ChimeraX Version: 1.8.dev202404160016 (2024-04-16 00:16:48 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8.dev202404160016 (2024-04-16)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/HeB2013-DOmainD-
> FPPR.cxs format session
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0256, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0309, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0214, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0359, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0813, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.512, step 1, values float32
Log from Sat Jun 8 00:54:17 2024UCSF ChimeraX version: 1.8.dev202404160016
(2024-04-16)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/YN2013-tr4-DomainD-
> FPPR.cxs
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0256, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.034, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0359, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0813, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.512, step 1, values float32
Log from Fri Jun 7 23:56:04 2024UCSF ChimeraX version: 1.8.dev202404160016
(2024-04-16)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/DomainD-
> FPPR.cxs
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0256, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.034, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0366, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0813, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.512, step 1, values float32
Log from Fri Jun 7 23:53:06 2024UCSF ChimeraX version: 1.8.dev202404160016
(2024-04-16)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/DomainD-C.cxs"
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0256, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.034, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0366, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0813, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.512, step 1, values float32
Log from Wed Dec 6 10:34:57 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/DomainD-C.cxs"
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0219, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.034, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0366, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0668, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.512, step 1, values float32
Log from Wed Dec 6 10:01:17 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/1205-overview.cxs" format session
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0219, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0244, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0366, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0668, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.55, step 1, values float32
Log from Tue Dec 5 22:13:05 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/overview.cxs"
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0219, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0244, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0366, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0668, step 1, values float32
Log from Tue Dec 5 20:42:09 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/1122-7.cxs
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0219, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0244, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0282, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0366, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0668, step 1, values float32
Log from Wed Nov 22 19:27:48 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-2.cxs
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0219, step 1, values float32
Log from Wed Nov 22 16:50:18 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-1.cxs
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Log from Wed Nov 22 16:25:43 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-1.cxs
> format session
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Log from Wed Nov 22 15:12:08 2023UCSF ChimeraX version: 1.5.dev202208242353
(2022-08-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/SUST_data_collection/tr1-dtm/20231121/polish+local-
> refinement /last_frame_rsr (7)-coot-
> EIC_NAG_real_space_refined_coot-1_real_space_refined.pdb"
Chain information for last_frame_rsr (7)-coot-
EIC_NAG_real_space_refined_coot-1_real_space_refined.pdb #1
---
Chain | Description
A B | No description available
C | No description available
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/SUST_data_collection/tr1-dtm/20231121/polish+local-
> refinement /relion_locres_filtered-job083.mrc"
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0145, step 1, values float32
> volume #2 level 0.04524
> volume #2 color #b2b2b231
> volume #2 color #b2b2b21d
> set bgColor white
> ui tool show "Model Panel"
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #1
25954 atoms, 26630 bonds, 12 pseudobonds, 3287 residues, 2 models selected
> DSSP
Unknown command: DSSP
> dssp
> select #1/B/C
17311 atoms, 17763 bonds, 8 pseudobonds, 2192 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select add #1
25954 atoms, 26630 bonds, 12 pseudobonds, 3287 residues, 2 models selected
> cartoon style (#!1 & sel) xsection rectangle modeHelix default
> select clear
> select #1 /A:18-298
2043 atoms, 2105 bonds, 3 pseudobonds, 255 residues, 2 models selected
> color (#!1 & sel) blue
> select #1 /A:321-515
1530 atoms, 1578 bonds, 195 residues, 1 model selected
> color sel cornflower blue
> select #1 /A:311-319,516-579
572 atoms, 582 bonds, 73 residues, 1 model selected
> color sel cyan
> select #1 /A:299-310,580-685
829 atoms, 847 bonds, 1 pseudobond, 110 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lime
> color sel spring green
> color sel lime
> color sel forest green
> color sel lime
> color sel green
> select #1 /A:686-1200
3386 atoms, 3454 bonds, 442 residues, 1 model selected
> color sel red
> select clear
> hide #!2 models
> ui tool show "Side View"
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide pseudobonds
> select clear
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20211017_TR2_DTM/atom
> selection from Kenya_TR2_DTM-coot-3-20231113.pdb"
Summary of feedback from opening
/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20211017_TR2_DTM/atom
selection from Kenya_TR2_DTM-coot-3-20231113.pdb
---
warnings | Ignored bad PDB record found on line 90
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 91
BOND : 0.008 0.072 27171
Ignored bad PDB record found on line 92
ANGLE : 1.010 12.611 37095
Ignored bad PDB record found on line 93
CHIRALITY : 0.066 0.416 4338
Ignored bad PDB record found on line 94
PLANARITY : 0.007 0.070 4749
15 messages similar to the above omitted
Chain information for atom selection from Kenya_TR2_DTM-coot-3-20231113.pdb #3
---
Chain | Description
A B C | No description available
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20211017_TR2_DTM/tr2_dtm_postprocess.mrc
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.00851, step 1, values float32
> volume #4 level 0.02062
> hide #!3 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> select clear
> select #1/A:1990@O3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1/A:1302@C7
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #1/A:1301@C2
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select add #1/A:906
51 atoms, 51 bonds, 4 residues, 1 model selected
> select up
200 atoms, 201 bonds, 23 residues, 1 model selected
> select clear
> select #1/B:539
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #1/A:1986@O4
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
3831 atoms, 3943 bonds, 484 residues, 1 model selected
> select down
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #1/A:1985@O5
43 atoms, 42 bonds, 4 residues, 1 model selected
> select add #1/A:1985@C5
44 atoms, 42 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> color sel blue
> select #1/A:1993@C4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1/A:1992@O3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
30 atoms, 30 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select add #1/A:1293@N2
43 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #1/C:813
77 atoms, 77 bonds, 6 residues, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #1/A:1297@C5
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel forest green
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1/A:1993@C4
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> color sel cornflower blue
> select clear
[Repeated 1 time(s)]
> select #1/A:1302@O3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3538 atoms, 3613 bonds, 458 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
30 atoms, 30 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select up
44 atoms, 44 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select add #1/A:1994@O4
57 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #1/A:1303@C2
71 atoms, 71 bonds, 6 residues, 1 model selected
> select up
73 atoms, 73 bonds, 6 residues, 1 model selected
> select down
71 atoms, 72 bonds, 6 residues, 1 model selected
> select up
73 atoms, 73 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
86 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> color sel red
> select clear
> select #1 /A
8643 atoms, 8867 bonds, 4 pseudobonds, 1095 residues, 2 models selected
> color (#!1 & sel) byhetero
> select clear
> ui mousemode right zoom
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/BM48-31-overview.png
> width 1977 height 1204 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1 /C:818-841
182 atoms, 185 bonds, 24 residues, 1 model selected
> color sel yellow
> select #1 /C:803-814
103 atoms, 104 bonds, 12 residues, 1 model selected
> color sel orange
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/BM48-31-overview.png
> width 1977 height 1204 supersample 3 transparentBackground true
> select #1 /C:803-814
103 atoms, 104 bonds, 12 residues, 1 model selected
> color sel light gray
> select #1 /C:866-910
335 atoms, 341 bonds, 45 residues, 1 model selected
> select #1 /C:820-842
175 atoms, 177 bonds, 23 residues, 1 model selected
> select #1 /C:818-841
182 atoms, 185 bonds, 24 residues, 1 model selected
> color sel light gray
> select #1 /C:820-842
175 atoms, 177 bonds, 23 residues, 1 model selected
> color sel yellow
> select #1 /C:803-819
138 atoms, 141 bonds, 17 residues, 1 model selected
> color sel orange
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/BM48-31-overview.png
> width 1977 height 1204 supersample 3 transparentBackground true
> show #!2 models
> select #2
4 models selected
> select clear
> hide #!2 models
> select #1/A:621
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> show #!2 models
> select #2
4 models selected
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/BM48-31-zoom.png
> width 1977 height 1204 supersample 3 transparentBackground true
> hide #!1 models
> show #!1 models
> hide #!2 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/BM48-31-overview-1.png
> width 1977 height 1204 supersample 4 transparentBackground true
> show #!4 models
> show #!2 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122.cxs
> show #!4 models
> show #!3 models
> hide #!1 models
> hide #!2 models
> volume #4 level 0.0224
> volume #4 level 0.02169
> ui tool show "Fit in Map"
> fitmap #4 inMap #2
Fit map tr2_dtm_postprocess.mrc in map relion_locres_filtered-job083.mrc using
40310 points
correlation = 0.9196, correlation about mean = 0.6049, overlap = 155.6
steps = 64, shift = 3.61, angle = 0.0633 degrees
Position of tr2_dtm_postprocess.mrc (#4) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99999941 -0.00108686 0.00009081 1.16637103
0.00108688 0.99999939 -0.00017394 0.76738113
-0.00009062 0.00017404 0.99999998 3.32934240
Axis 0.15753984 0.08213784 0.98409074
Axis point -439.47459951 562.71555553 0.00000000
Rotation angle (degrees) 0.06327989
Shift along axis 3.52315594
> hide #!3 models
> fitmap #3 inMap #4
Fit molecule atom selection from Kenya_TR2_DTM-coot-3-20231113.pdb (#3) to map
tr2_dtm_postprocess.mrc (#4) using 26545 atoms
average map value = 0.03663, steps = 56
shifted from previous position = 3.61
rotated from previous position = 0.0649 degrees
atoms outside contour = 5684, contour level = 0.021692
Position of atom selection from Kenya_TR2_DTM-coot-3-20231113.pdb (#3)
relative to tr2_dtm_postprocess.mrc (#4) coordinates:
Matrix rotation and translation
1.00000000 0.00001167 0.00008522 -0.02454614
-0.00001166 0.99999999 -0.00013522 0.04200844
-0.00008522 0.00013522 0.99999999 -0.01330735
Axis 0.84375657 0.53176639 -0.07279671
Axis point 0.00000000 97.04535290 300.45449226
Rotation angle (degrees) 0.00918202
Shift along axis 0.00259644
> show #!3 models
> hide #!2 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> dssp
> select clear
> show #!1 models
> hide #!1 models
> select #3/B/C
17688 atoms, 18158 bonds, 2 pseudobonds, 2234 residues, 2 models selected
> color (#!3 & sel) light gray
> select #3/A
8857 atoms, 9093 bonds, 1 pseudobond, 1118 residues, 2 models selected
> select #3/A:17-297
2246 atoms, 2313 bonds, 281 residues, 1 model selected
> color sel blue
> select #3/A:320-517
1546 atoms, 1594 bonds, 198 residues, 1 model selected
> volume #2 color #4f8f00
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> show #!2 models
> hide #!2 models
> select #3/A:310-319
78 atoms, 79 bonds, 10 residues, 1 model selected
> select #3/A:310-319,518-581
583 atoms, 595 bonds, 74 residues, 1 model selected
> color sel cyan
> select clear
> select #3/A:298-309,582-684
873 atoms, 890 bonds, 115 residues, 1 model selected
> color sel forest green
> select #3/A:685-1200
3609 atoms, 3681 bonds, 1 pseudobond, 450 residues, 2 models selected
> select #3/A:685-1100
3087 atoms, 3145 bonds, 1 pseudobond, 400 residues, 2 models selected
> select #3/A:685-1159
3609 atoms, 3681 bonds, 1 pseudobond, 450 residues, 2 models selected
> select #3/A:685-1125
3273 atoms, 3335 bonds, 1 pseudobond, 425 residues, 2 models selected
> select #3/A:685-1126
3282 atoms, 3344 bonds, 1 pseudobond, 426 residues, 2 models selected
> color sel red
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> cartoon style (#!3 & sel) xsection rectangle modeHelix default
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #2 color silver
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-1.cxs
——— End of log from Wed Nov 22 15:12:08 2023 ———
opened ChimeraX session
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
6549 atoms, 6739 bonds, 819 residues, 1 model selected
> select up
6573 atoms, 6762 bonds, 822 residues, 1 model selected
> select up
8857 atoms, 9093 bonds, 1118 residues, 1 model selected
> select up
26545 atoms, 27251 bonds, 3352 residues, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #3/A:1140@C5
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel forest green
> select #3/A:1144@C6
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
6549 atoms, 6739 bonds, 819 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #3/A:1145@C5
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
31 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #3/A:1146@N2
43 atoms, 42 bonds, 4 residues, 1 model selected
> select subtract #3/A:1146@N2
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #3/A:1146@C2
43 atoms, 42 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
8857 atoms, 9093 bonds, 1118 residues, 1 model selected
> select up
26545 atoms, 27251 bonds, 3352 residues, 1 model selected
> select up
52499 atoms, 53881 bonds, 6639 residues, 6 models selected
> select down
26545 atoms, 27251 bonds, 3352 residues, 1 model selected
> select down
8857 atoms, 9093 bonds, 1118 residues, 1 model selected
> select down
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 70 bonds, 5 residues, 1 model selected
> color sel red
> select #3/A:1137@C3
1 atom, 1 residue, 1 model selected
> select #3/C:565
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #3/A:1128@C8
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #3/A:1134@C5
57 atoms, 56 bonds, 5 residues, 1 model selected
> select subtract #3/A:1134@C5
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #3/A:1134@C6
57 atoms, 56 bonds, 5 residues, 1 model selected
> select up
70 atoms, 70 bonds, 5 residues, 1 model selected
> select up
72 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 84 bonds, 6 residues, 1 model selected
> select up
6549 atoms, 6739 bonds, 819 residues, 1 model selected
> select down
84 atoms, 84 bonds, 6 residues, 1 model selected
> select add #3/A:1131@O7
85 atoms, 84 bonds, 7 residues, 1 model selected
> select up
98 atoms, 98 bonds, 7 residues, 1 model selected
> select add #3/A:1130@O6
99 atoms, 98 bonds, 8 residues, 1 model selected
> select up
112 atoms, 113 bonds, 8 residues, 1 model selected
> select add #3/A:1135@C4
113 atoms, 113 bonds, 9 residues, 1 model selected
> select add #3/A:1135@C5
114 atoms, 113 bonds, 9 residues, 1 model selected
> select up
126 atoms, 127 bonds, 9 residues, 1 model selected
> select up
6549 atoms, 6739 bonds, 819 residues, 1 model selected
> select down
126 atoms, 127 bonds, 9 residues, 1 model selected
> select up
128 atoms, 128 bonds, 10 residues, 1 model selected
> select up
140 atoms, 142 bonds, 10 residues, 1 model selected
> select add #3/A:1148@O5
141 atoms, 142 bonds, 11 residues, 1 model selected
> select add #3/A:1148@O6
142 atoms, 142 bonds, 11 residues, 1 model selected
> select add #3/C:339
148 atoms, 147 bonds, 12 residues, 1 model selected
> select subtract #3/C:339
142 atoms, 142 bonds, 11 residues, 1 model selected
> select up
144 atoms, 143 bonds, 12 residues, 1 model selected
> select up
162 atoms, 165 bonds, 12 residues, 1 model selected
> select add #3/A:1149@C6
163 atoms, 165 bonds, 13 residues, 1 model selected
> select up
173 atoms, 178 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel blue
> select clear
> select #3/A:1127@O3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #3/A:1138@O5
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> ui tool show "Model Panel"
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3/A
8857 atoms, 9093 bonds, 1 pseudobond, 1118 residues, 2 models selected
> color (#!3 & sel) byhetero
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> hide pseudobonds
> select clear
> select #3/B: 819-831
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/B: 819-841
88 atoms, 88 bonds, 11 residues, 1 model selected
> color sel yellow
> select #3/B: 802-819
110 atoms, 111 bonds, 13 residues, 1 model selected
> color sel orange
> select clear
> show #!1 models
> ui mousemode right zoom
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-1.cxs
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/PDB
> /Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
> coot-3-20230529.pdb"
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/laos_20_52/relion_locres_filtered.mrc
Chain information for
Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-coot-3-20230529.pdb
#5
---
Chain | Description
A C | No description available
B | No description available
Opened relion_locres_filtered.mrc as #6, grid size 256,256,256, pixel 1.32,
shown at level 0.0194, step 1, values float32
> hide #!3 models
> hide #!1 models
> volume #6 level 0.04259
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/laos_20_52
> 2/postprocess.mrc"
Opened postprocess.mrc as #7, grid size 256,256,256, pixel 1.32, shown at
level 0.0138, step 1, values float32
> volume #7 level 0.0209
> close #6
> volume #7 level 0.01955
> close #7
> select add #5
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> select subtract #5
Nothing selected
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/postprocessing/laos_20_52_job033_postprocess.mrc
Opened laos_20_52_job033_postprocess.mrc as #6, grid size 256,256,256, pixel
1.32, shown at level 0.0138, step 1, values float32
> volume #6 level 0.02361
> volume #6 level 0.01752
> volume #6 level 0.02259
> ui tool show "Fit in Map"
> fitmap #6 inMap #2
Fit map laos_20_52_job033_postprocess.mrc in map relion_locres_filtered-
job083.mrc using 68687 points
correlation = 0.8556, correlation about mean = 0.447, overlap = 237.8
steps = 296, shift = 75.1, angle = 1.34 degrees
Position of laos_20_52_job033_postprocess.mrc (#6) relative to
relion_locres_filtered-job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99972581 -0.02341475 0.00023353 46.21025889
0.02341480 0.99972581 -0.00023524 38.37180932
-0.00022796 0.00024064 0.99999995 45.52436735
Axis 0.01016086 0.00985362 0.99989983
Axis point -1596.17759724 1972.12390580 0.00000000
Rotation angle (degrees) 1.34182480
Shift along axis 46.36744416
> fitmap #5 inMap #6
Fit molecule Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) to map laos_20_52_job033_postprocess.mrc (#6) using
26908 atoms
average map value = 0.01023, steps = 456
shifted from previous position = 69.2
rotated from previous position = 8.76 degrees
atoms outside contour = 21756, contour level = 0.022593
Position of Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) relative to laos_20_52_job033_postprocess.mrc (#6)
coordinates:
Matrix rotation and translation
0.99162679 -0.12913650 -0.00027693 23.20505151
0.12913463 0.99162030 -0.00366387 -19.79146132
0.00074775 0.00359743 0.99999325 -11.19236848
Axis 0.02810373 -0.00396587 0.99959714
Axis point 164.69864000 171.29070896 0.00000000
Rotation angle (degrees) 7.42264971
Shift along axis -10.45722075
> fitmap #5 inMap #6
Fit molecule Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) to map laos_20_52_job033_postprocess.mrc (#6) using
26908 atoms
average map value = 0.01023, steps = 28
shifted from previous position = 0.0291
rotated from previous position = 0.0163 degrees
atoms outside contour = 21767, contour level = 0.022593
Position of Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) relative to laos_20_52_job033_postprocess.mrc (#6)
coordinates:
Matrix rotation and translation
0.99163950 -0.12903819 -0.00050425 23.22312797
0.12903564 0.99163370 -0.00352274 -19.79721327
0.00095460 0.00342823 0.99999367 -11.22775860
Axis 0.02692384 -0.00565067 0.99962152
Axis point 165.00111299 171.46838396 0.00000000
Rotation angle (degrees) 7.41676573
Shift along axis -10.48638575
> select add #5
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> select add #6
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 6 models selected
> close #6
> close #5
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/PDB
> /Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
> coot-3-20230529.pdb"
Chain information for
Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-coot-3-20230529.pdb
#5
---
Chain | Description
A C | No description available
B | No description available
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/laos_20_52
> 2/postprocess.mrc"
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0138, step 1, values float32
> volume #6 level 0.02395
> ui tool show "Model Panel"
> fitmap #6 inMap #2
Fit map postprocess.mrc in map relion_locres_filtered-job083.mrc using 64066
points
correlation = 0.8585, correlation about mean = 0.4322, overlap = 233.6
steps = 308, shift = 75.1, angle = 1.34 degrees
Position of postprocess.mrc (#6) relative to relion_locres_filtered-job083.mrc
(#2) coordinates:
Matrix rotation and translation
0.99972581 -0.02341451 0.00024744 46.18490597
0.02341453 0.99972584 -0.00008366 38.34052627
-0.00024541 0.00008943 0.99999997 45.55289988
Axis 0.00369599 0.01052369 0.99993779
Axis point -1593.50727033 1983.87018044 0.00000000
Rotation angle (degrees) 1.34175941
Shift along axis 46.12424881
> fitmap #5 inMap #6
Fit molecule Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) to map postprocess.mrc (#6) using 26908 atoms
average map value = 0.01023, steps = 452
shifted from previous position = 69.2
rotated from previous position = 8.77 degrees
atoms outside contour = 22041, contour level = 0.023945
Position of Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) relative to postprocess.mrc (#6) coordinates:
Matrix rotation and translation
0.99162407 -0.12915711 -0.00037569 23.22795080
0.12915492 0.99161779 -0.00362886 -19.79945242
0.00084123 0.00354994 0.99999335 -11.21546200
Axis 0.02778019 -0.00470918 0.99960296
Axis point 164.80627630 171.40730538 0.00000000
Rotation angle (degrees) 7.42378866
Shift along axis -10.47249307
> ui tool show "Model Panel"
> hide #!5 models
> show #!2 models
> hide #!6 models
> show #!5 models
> hide #!2 models
> show #!6 models
> select add #5
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.98833,-0.15234,-4.3183e-05,68.038,0.15234,0.98832,-0.0037203,19.368,0.00060943,0.0036703,0.99999,43.956
> select add #6
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 6 models selected
> select subtract #5
4 models selected
> select subtract #6
Nothing selected
> fitmap #5 inMap #6
Fit molecule Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) to map postprocess.mrc (#6) using 26908 atoms
average map value = 0.04346, steps = 88
shifted from previous position = 2.1
rotated from previous position = 7.42 degrees
atoms outside contour = 5447, contour level = 0.023945
Position of Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb (#5) relative to postprocess.mrc (#6) coordinates:
Matrix rotation and translation
1.00000000 0.00000606 -0.00005740 0.01047371
-0.00000605 1.00000000 0.00008944 -0.00911450
0.00005740 -0.00008944 0.99999999 -0.00849089
Axis -0.84023700 -0.53922689 -0.05688706
Axis point 0.00000000 -97.11013599 122.42088454
Rotation angle (degrees) 0.00609866
Shift along axis -0.00340260
> hide #!6 models
> show #!3 models
> show #!1 models
> dssp
> select add #5
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> select add #5
53453 atoms, 54861 bonds, 15 pseudobonds, 6737 residues, 4 models selected
> select subtract #5
26545 atoms, 27251 bonds, 3 pseudobonds, 3352 residues, 2 models selected
> select add #5
53453 atoms, 54861 bonds, 15 pseudobonds, 6737 residues, 4 models selected
> select add #1
79407 atoms, 81491 bonds, 27 pseudobonds, 10024 residues, 6 models selected
> dssp
> select clear
[Repeated 1 time(s)]
> show #!6 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #6 color #d6d6d6
> volume #6 color #d6d6d626
> ui mousemode right zoom
> volume #6 level 0.0259
> ui tool show "Model Panel"
> select add #5
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> select add #6
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 6 models selected
> select subtract #6
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> hide #!6 models
> show #!3 models
> show #!1 models
> select add #1
52862 atoms, 54240 bonds, 24 pseudobonds, 6672 residues, 4 models selected
> select add #3
79407 atoms, 81491 bonds, 27 pseudobonds, 10024 residues, 6 models selected
> cartoon style (#!1,3,5 & sel) xsection rectangle modeHelix default
> select clear
> cartoon style width 2.5 thickness 0.45
> cartoon style width 3.5 thickness 0.45
> cartoon style width 2.5 thickness 0.45
> hide #!3 models
> hide #!1 models
> select add #5
26908 atoms, 27610 bonds, 12 pseudobonds, 3385 residues, 2 models selected
> hide pseudobonds
> select clear
> select #5/A/B
17933 atoms, 18401 bonds, 7 pseudobonds, 2256 residues, 2 models selected
> color (#!5 & sel) light gray
> select clear
> select #5/C:13-307
2331 atoms, 2400 bonds, 1 pseudobond, 288 residues, 2 models selected
> color (#!5 & sel) blue
> select #5/C:1397@O4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #5/C:1902@C4
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #5/C:1300@N2
43 atoms, 42 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select up
72 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select add #5/C:1697@C3
85 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> select up
5371 atoms, 5530 bonds, 669 residues, 1 model selected
> select down
98 atoms, 99 bonds, 7 residues, 1 model selected
> select down
85 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> select add #5/C:1298@O6
99 atoms, 99 bonds, 8 residues, 1 model selected
> select up
112 atoms, 113 bonds, 8 residues, 1 model selected
> color sel blue
> select clear
> select #5/C:326-524
1582 atoms, 1630 bonds, 199 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select #5/C:1898@C5
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #5/C:1497@C2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #5/C:1497@O6
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #5/C:1302@O4
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel royal blue
[Repeated 2 time(s)]
> select #5/C:1797@C7
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select #5/C:317-326,525-588
579 atoms, 587 bonds, 74 residues, 1 model selected
> color sel cyan
> select #5/C:304-315,589-691
800 atoms, 817 bonds, 1 pseudobond, 107 residues, 2 models selected
> color (#!5 & sel) forest green
> select #5/C:1305@C4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel green
[Repeated 1 time(s)]
> select clear
> select #5/C:692-1136
3390 atoms, 3455 bonds, 1 pseudobond, 442 residues, 2 models selected
> color sel red
> select up
3429 atoms, 3495 bonds, 1 pseudobond, 447 residues, 2 models selected
> select clear
> select #5/C:13-307
2331 atoms, 2400 bonds, 1 pseudobond, 288 residues, 2 models selected
> select #5/C:330-528
1571 atoms, 1619 bonds, 199 residues, 1 model selected
> color sel royal blue
> select #5/C:320-330,529-592
589 atoms, 600 bonds, 75 residues, 1 model selected
> color sel cyan
> select #5/C:308-319,593-695
802 atoms, 817 bonds, 1 pseudobond, 107 residues, 2 models selected
> color sel forest green
> select #5/C:696-1136
3361 atoms, 3426 bonds, 1 pseudobond, 438 residues, 2 models selected
> select clear
> select #5/C:830-852
177 atoms, 179 bonds, 23 residues, 1 model selected
> select #5/B:830-852
160 atoms, 162 bonds, 21 residues, 1 model selected
> color sel yellow
> select #5/B:812-827
122 atoms, 123 bonds, 15 residues, 1 model selected
> color sel orange
> select clear
> select #5/C
8975 atoms, 9209 bonds, 3 pseudobonds, 1129 residues, 2 models selected
> color (#!5 & sel) byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
1164 atoms, 1189 bonds, 147 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
1164 atoms, 1189 bonds, 147 residues, 1 model selected
> select down
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
31 atoms, 31 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select up
44 atoms, 44 bonds, 4 residues, 1 model selected
> select up
56 atoms, 58 bonds, 4 residues, 1 model selected
> select up
58 atoms, 59 bonds, 5 residues, 1 model selected
> select up
70 atoms, 72 bonds, 5 residues, 1 model selected
> select add #5/C:1313@C3
71 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 87 bonds, 6 residues, 1 model selected
> select up
86 atoms, 88 bonds, 7 residues, 1 model selected
> select up
98 atoms, 101 bonds, 7 residues, 1 model selected
> select add #5/C:1307@C4
99 atoms, 101 bonds, 8 residues, 1 model selected
> select add #5/C:1307@C6
100 atoms, 101 bonds, 8 residues, 1 model selected
> select up
112 atoms, 115 bonds, 8 residues, 1 model selected
> select add #5/C:1316@C5
113 atoms, 115 bonds, 9 residues, 1 model selected
> select up
126 atoms, 129 bonds, 9 residues, 1 model selected
> select up
128 atoms, 130 bonds, 10 residues, 1 model selected
> select up
140 atoms, 144 bonds, 10 residues, 1 model selected
> color sel red
> color sel byhetero
> select clear
> ui tool show "Model Panel"
> show #!3 models
> show #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-1.cxs
——— End of log from Wed Nov 22 16:25:43 2023 ———
opened ChimeraX session
> ui tool show "Model Panel"
[Repeated 1 time(s)]
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_236/aos_20_236_RealSpaceRefine_3_atom_selection_from_laos_20_236_chainABC-
> coot-20220620-changedNAG.pdb
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_236/laos_20_236_job019_postprocess.mrc
Chain information for
aos_20_236_RealSpaceRefine_3_atom_selection_from_laos_20_236_chainABC-
coot-20220620-changedNAG.pdb #7
---
Chain | Description
A B C | No description available
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.013, step 1, values float32
> hide #!5 models
> hide #!3 models
> hide #!1 models
> volume #8 level 0.02191
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #8 inMap #2
Fit map laos_20_236_job019_postprocess.mrc in map relion_locres_filtered-
job083.mrc using 92523 points
correlation = 0.8079, correlation about mean = 0.3175, overlap = 245.3
steps = 240, shift = 71, angle = 4.61 degrees
Position of laos_20_236_job019_postprocess.mrc (#8) relative to
relion_locres_filtered-job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99676097 -0.08042098 0.00019878 56.34425871
0.08042108 0.99676080 -0.00059622 29.31885092
-0.00015019 0.00061027 0.99999980 38.20361450
Axis 0.00750087 0.00216958 0.99996951
Axis point -334.90561173 710.49657474 0.00000000
Rotation angle (degrees) 4.61290799
Shift along axis 38.68869027
> fitmap #7 inMap #8
Fit molecule
aos_20_236_RealSpaceRefine_3_atom_selection_from_laos_20_236_chainABC-
coot-20220620-changedNAG.pdb (#7) to map laos_20_236_job019_postprocess.mrc
(#8) using 26337 atoms
average map value = 0.04289, steps = 296
shifted from previous position = 70.9
rotated from previous position = 4.65 degrees
atoms outside contour = 3614, contour level = 0.021915
Position of
aos_20_236_RealSpaceRefine_3_atom_selection_from_laos_20_236_chainABC-
coot-20220620-changedNAG.pdb (#7) relative to
laos_20_236_job019_postprocess.mrc (#8) coordinates:
Matrix rotation and translation
0.99999950 -0.00064646 0.00075974 -0.10977492
0.00064634 0.99999978 0.00015017 -0.16047326
-0.00075984 -0.00014968 0.99999970 0.14846764
Axis -0.14861933 0.75319473 0.64078857
Axis point 203.27657792 0.00000000 146.46463907
Rotation angle (degrees) 0.05779764
Shift along axis -0.00941658
> hide #!2 models
> volume #8 color #b2b2b227
> volume #8 color #b2b2b229
> hide #!8 models
> show #!5 models
> select add #7
26337 atoms, 26941 bonds, 12 pseudobonds, 3333 residues, 2 models selected
> dssp
> hide pseudobonds
> select clear
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> cartoon style width 2.5 thickness 0.45
> select clear
> hide #!5 models
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #7/B/C
17558 atoms, 17950 bonds, 8 pseudobonds, 2222 residues, 2 models selected
> color (#!7 & sel) light gray
> select clear
> select #7/A:13-307
2232 atoms, 2293 bonds, 2 pseudobonds, 279 residues, 2 models selected
> color (#!7 & sel) blue
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #7/A:1698@C6
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #7/C:375
48 atoms, 47 bonds, 4 residues, 1 model selected
> select add #7/C:422
55 atoms, 54 bonds, 5 residues, 1 model selected
> select subtract #7/C:375
49 atoms, 49 bonds, 4 residues, 1 model selected
> select add #7/C:374
58 atoms, 57 bonds, 5 residues, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
4661 atoms, 4792 bonds, 585 residues, 1 model selected
> select down
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #7/C:428
62 atoms, 61 bonds, 5 residues, 1 model selected
> select subtract #7/C:428
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #7/A:1701@C4
57 atoms, 56 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select up
72 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
86 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> select up
100 atoms, 100 bonds, 8 residues, 1 model selected
> select up
112 atoms, 113 bonds, 8 residues, 1 model selected
> color sel blue
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #7/A:326-524
1571 atoms, 1616 bonds, 199 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select #7/A:317-326，525-588
Expected an objects specifier or a keyword
> select #7/A:317-326, 525-588
581 atoms, 591 bonds, 74 residues, 1 model selected
> color sel cyan
> select #7/A:304-315,589-691
802 atoms, 815 bonds, 1 pseudobond, 107 residues, 2 models selected
> color (#!7 & sel) forest green
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel green
> select add #7/A:1704@C7
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel royal blue
> select clear
> select #7/A:316
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel forest green
> select clear
> select #7/A:1708@C5
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel forest green
> select clear
> select #7/A:692-1132
3342 atoms, 3402 bonds, 1 pseudobond, 436 residues, 2 models selected
> color (#!7 & sel) red
> select clear
> select #7/A:1307@C2
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
30 atoms, 30 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select add #7/A:1711@C5
43 atoms, 43 bonds, 4 residues, 1 model selected
> select add #7/A:1711@C4
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #7/A:1713@C4
71 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select add #7/A:1712@O3
85 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> color sel red
> select #7/A
8779 atoms, 8991 bonds, 4 pseudobonds, 1111 residues, 2 models selected
> color (#!7 & sel) byhetero
> select clear
> ui tool show "Model Panel"
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!7 models
> select #1/A:330-528
1563 atoms, 1608 bonds, 199 residues, 1 model selected
> select #1/A: 330-528
1563 atoms, 1608 bonds, 199 residues, 1 model selected
> select #1/A: 321-515
1530 atoms, 1578 bonds, 195 residues, 1 model selected
> select up
1532 atoms, 1579 bonds, 196 residues, 1 model selected
> select up
1544 atoms, 1592 bonds, 196 residues, 1 model selected
> select up
1546 atoms, 1593 bonds, 197 residues, 1 model selected
> select up
1558 atoms, 1606 bonds, 197 residues, 1 model selected
> select up
1560 atoms, 1607 bonds, 198 residues, 1 model selected
> select up
1572 atoms, 1622 bonds, 198 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel byhetero
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-2.cxs
——— End of log from Wed Nov 22 16:50:18 2023 ———
opened ChimeraX session
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/TR5_GX2013/WT_structure/20230227/tr5_dtm.pdb
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/TR5_GX2013/WT_structure/postprocess.mrc
Chain information for tr5_dtm.pdb #9
---
Chain | Description
A C | No description available
B | No description available
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0162, step 1, values float32
> ui tool show "Model Panel"
> hide #!1 models
> volume #10 level 0.02437
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #10 inMap #2
Fit map postprocess.mrc in map relion_locres_filtered-job083.mrc using 84252
points
correlation = 0.7981, correlation about mean = 0.291, overlap = 249.8
steps = 312, shift = 88, angle = 4.99 degrees
Position of postprocess.mrc (#10) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99621038 -0.08697605 0.00020549 67.14751386
0.08697611 0.99621035 -0.00031455 39.67322706
-0.00017735 0.00033123 0.99999993 46.53837842
Axis 0.00371241 0.00220078 0.99999069
Axis point -420.60399066 788.34833115 0.00000000
Rotation angle (degrees) 4.98971359
Shift along axis 46.87453574
> fitmap #9 inMap #10
Fit molecule tr5_dtm.pdb (#9) to map postprocess.mrc (#10) using 25312 atoms
average map value = 4.301e-05, steps = 88
shifted from previous position = 1.79
rotated from previous position = 1.66 degrees
atoms outside contour = 24959, contour level = 0.024367
Position of tr5_dtm.pdb (#9) relative to postprocess.mrc (#10) coordinates:
Matrix rotation and translation
0.99408575 0.10667917 -0.02032423 -70.33988920
-0.10656027 0.99428266 0.00684914 -31.51468998
0.02093869 -0.00464288 0.99976998 -47.37614713
Axis -0.05283716 -0.18971559 -0.98041636
Axis point -228.99307088 618.85643620 0.00000000
Rotation angle (degrees) 6.24323075
Shift along axis 56.14373739
> select add #9
25312 atoms, 25883 bonds, 15 pseudobonds, 3187 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.99996,-0.0068264,-0.0060012,1.7803,0.0072133,0.99773,0.06702,-10.684,0.00553,-0.067061,0.99773,11.592
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.99996,-0.0068264,-0.0060012,33.788,0.0072133,0.99773,0.06702,-17.941,0.00553,-0.067061,0.99773,57.151
> view matrix models
> #9,0.99996,-0.0068264,-0.0060012,35.823,0.0072133,0.99773,0.06702,-18.449,0.00553,-0.067061,0.99773,56.886
> select subtract #9
Nothing selected
> fitmap #9 inMap #10
Fit molecule tr5_dtm.pdb (#9) to map postprocess.mrc (#10) using 25312 atoms
average map value = 0.04671, steps = 292
shifted from previous position = 62.7
rotated from previous position = 6.02 degrees
atoms outside contour = 4614, contour level = 0.024367
Position of tr5_dtm.pdb (#9) relative to postprocess.mrc (#10) coordinates:
Matrix rotation and translation
0.99999996 -0.00028356 0.00007014 0.02399836
0.00028357 0.99999996 -0.00006459 -0.03092390
-0.00007012 0.00006461 1.00000000 0.50622927
Axis 0.21593562 0.23441507 0.94785093
Axis point 503.96077655 -279.26483737 0.00000000
Rotation angle (degrees) 0.01714098
Shift along axis 0.47776296
> hide #!2 models
> hide #!10 models
> show #!1 models
> hide p
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> cartoon style width 2.5 thickness 0.45
> select clear
> select add #9
25312 atoms, 25883 bonds, 15 pseudobonds, 3187 residues, 2 models selected
> dssp
> select clear
> hide #!1 models
> select #9/B/C
16877 atoms, 17262 bonds, 10 pseudobonds, 2125 residues, 2 models selected
> select #9/B/A
16876 atoms, 17257 bonds, 10 pseudobonds, 2125 residues, 2 models selected
> color (#!9 & sel) light gray
> select clear
> select #9/C:
Expected an objects specifier or a keyword
> select #9/C:17-298
1931 atoms, 1975 bonds, 4 pseudobonds, 237 residues, 2 models selected
> color (#!9 & sel) blue
> select #9/C:321-501
1439 atoms, 1478 bonds, 181 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #9/C:311-321.502-565
Expected an objects specifier or a keyword
> select #9/C:311-321,502-565
593 atoms, 604 bonds, 75 residues, 1 model selected
> color sel cyan
> select #9/C:299-310,566-668
799 atoms, 812 bonds, 107 residues, 1 model selected
> color sel forest green
> select #9/C:669-1110
3387 atoms, 3448 bonds, 442 residues, 1 model selected
> color sel red
> select #9/A:803-825
179 atoms, 180 bonds, 23 residues, 1 model selected
> color sel yellow
> select #9/A:786-802
135 atoms, 137 bonds, 17 residues, 1 model selected
> color sel orange
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select up
72 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select add #9/C:1401@C1
85 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> color sel blue
> select #9/C:1306@C7
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #9/C:1306@O4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select add #9/C:1309@O3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9/C:1310@C4
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel forest green
> select add #9/C:1311@O4
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 70 bonds, 5 residues, 1 model selected
> select up
72 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 84 bonds, 6 residues, 1 model selected
> select up
86 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 98 bonds, 7 residues, 1 model selected
> select up
100 atoms, 99 bonds, 8 residues, 1 model selected
> select up
112 atoms, 113 bonds, 8 residues, 1 model selected
> select up
114 atoms, 114 bonds, 9 residues, 1 model selected
> select up
126 atoms, 127 bonds, 9 residues, 1 model selected
> select add #9/C:1314@C3
127 atoms, 127 bonds, 10 residues, 1 model selected
> select up
129 atoms, 129 bonds, 10 residues, 1 model selected
> select up
140 atoms, 142 bonds, 10 residues, 1 model selected
> select add #9/C:765@OD1
141 atoms, 142 bonds, 11 residues, 1 model selected
> select up
148 atoms, 149 bonds, 11 residues, 1 model selected
> select up
420 atoms, 431 bonds, 45 residues, 1 model selected
> select down
148 atoms, 149 bonds, 11 residues, 1 model selected
> select down
141 atoms, 142 bonds, 11 residues, 1 model selected
> select up
143 atoms, 143 bonds, 12 residues, 1 model selected
> select up
162 atoms, 164 bonds, 12 residues, 1 model selected
> color sel red
> select clear
> select #9/C:1310@C4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #9/C:1309@C3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select subtract #9/C:1309@C3
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel forest green
> select #9/C
8436 atoms, 8626 bonds, 5 pseudobonds, 1062 residues, 2 models selected
> color (#!9 & sel) byhetero
> select clear
> show #!7 models
> show #!5 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> hide #!5 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> show #!2 models
> hide #!2 models
> show #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-3.cxs
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20220223_HeB/HeB2013_20230620_edit_add360N.pdb
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20220223_HeB/postprocess.mrc
Summary of feedback from opening
/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20220223_HeB/HeB2013_20230620_edit_add360N.pdb
---
warnings | Ignored bad PDB record found on line 89
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 90
BOND : 0.016 1.141 26481
Ignored bad PDB record found on line 91
ANGLE : 1.174 23.400 36161
Ignored bad PDB record found on line 92
CHIRALITY : 0.078 0.804 4295
Ignored bad PDB record found on line 93
PLANARITY : 0.008 0.107 4610
15 messages similar to the above omitted
Chain information for HeB2013_20230620_edit_add360N.pdb #11
---
Chain | Description
A B C | No description available
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.00741, step 1, values float32
> volume #12 level 0.01365
> hide #!9 models
> hide #!1 models
> volume #12 color #d6d6d6
> volume #12 level 0.01865
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> fitmap #12 inMap #2
Fit map postprocess.mrc in map relion_locres_filtered-job083.mrc using 54591
points
correlation = 0.9066, correlation about mean = 0.6581, overlap = 201.1
steps = 68, shift = 3.17, angle = 0.998 degrees
Position of postprocess.mrc (#12) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99984828 -0.01741810 0.00016392 4.62467797
0.01741811 0.99984829 -0.00007043 -2.66255625
-0.00016267 0.00007328 0.99999998 2.88057744
Axis 0.00412497 0.00937457 0.99994755
Axis point 156.70323681 263.46425244 0.00000000
Rotation angle (degrees) 0.99808653
Shift along axis 2.87454266
> fitmap #11 inMap #12
Fit molecule HeB2013_20230620_edit_add360N.pdb (#11) to map postprocess.mrc
(#12) using 25953 atoms
average map value = 0.04561, steps = 56
shifted from previous position = 3.16
rotated from previous position = 0.987 degrees
atoms outside contour = 2397, contour level = 0.018646
Position of HeB2013_20230620_edit_add360N.pdb (#11) relative to
postprocess.mrc (#12) coordinates:
Matrix rotation and translation
0.99999994 0.00018774 -0.00030010 0.00442002
-0.00018769 0.99999997 0.00016691 -0.02226537
0.00030013 -0.00016685 0.99999994 -0.02492634
Axis -0.42641910 -0.76687536 -0.47965501
Axis point 39.67861952 0.00000000 53.29282567
Rotation angle (degrees) 0.02242254
Shift along axis 0.02714603
> volume #12 level 0.02822
> hide #!12 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select add #11
25953 atoms, 26619 bonds, 9 pseudobonds, 3267 residues, 2 models selected
> dssp
> hide pesudobonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select clear
> select add #11
25953 atoms, 26619 bonds, 9 pseudobonds, 3267 residues, 2 models selected
> cartoon style (#!11 & sel) xsection rectangle modeHelix default
> select clear
> select #11/B
8651 atoms, 8873 bonds, 3 pseudobonds, 1089 residues, 2 models selected
> select #11/A /C
17302 atoms, 17746 bonds, 6 pseudobonds, 2178 residues, 2 models selected
> color (#!11 & sel) light gray
> select clear
> select #11/B:17-298
2065 atoms, 2118 bonds, 2 pseudobonds, 257 residues, 2 models selected
> color (#!11 & sel) blue
> select clear
> select #11/B:321-500
1443 atoms, 1486 bonds, 180 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #11/B:311-321,501-564
590 atoms, 602 bonds, 75 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> select #11/B:299-310,565-667
799 atoms, 817 bonds, 1 pseudobond, 107 residues, 2 models selected
> color sel forest green
> select #11/B:668-1115
3439 atoms, 3507 bonds, 448 residues, 1 model selected
> color sel red
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
3636 atoms, 3713 bonds, 467 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #11/B:1716@C2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select up
44 atoms, 44 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select add #11/B:1712@C3
57 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 72 bonds, 5 residues, 1 model selected
> select up
72 atoms, 73 bonds, 6 residues, 1 model selected
> select up
84 atoms, 86 bonds, 6 residues, 1 model selected
> select add #11/B:1715@N2
85 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 100 bonds, 7 residues, 1 model selected
> select up
100 atoms, 101 bonds, 8 residues, 1 model selected
> select up
112 atoms, 115 bonds, 8 residues, 1 model selected
> color sel red
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel forest green
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #11/B:1718@C3
43 atoms, 42 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
3241 atoms, 3334 bonds, 408 residues, 1 model selected
> select down
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select up
72 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
86 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 100 bonds, 7 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
Drag select of 2 residues
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #11/B:1703@C4
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #11/B:1706@C2
43 atoms, 42 bonds, 4 residues, 1 model selected
> select subtract #11/B:1706@C2
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #11/B:1706@N2
43 atoms, 42 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #11/B:1702@N2
71 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
5015 atoms, 5160 bonds, 622 residues, 1 model selected
> select down
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #11/B:1704@C5
15 atoms, 14 bonds, 2 residues, 1 model selected
> select subtract #11/B:1704@C5
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #11/B:1702@C7
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #11/B:1706@C4
57 atoms, 56 bonds, 5 residues, 1 model selected
> select subtract #11/B:1706@C4
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #11/B:1706@O3
57 atoms, 56 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select up
72 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select add #11/B:1707@N2
85 atoms, 85 bonds, 7 residues, 1 model selected
> select #11/B:1707@N2
1 atom, 1 residue, 1 model selected
> select #11/B:1309@C3
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #11/B:1308@C3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> color sel forest green
> view matrix models
> #11,0.99985,-0.01723,-0.00013904,11.108,0.01723,0.99985,9.1223e-05,-11.519,0.00013745,-9.3605e-05,1,-2.1503
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #11/B:1706@C2
57 atoms, 56 bonds, 5 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #11/B:1702@C7
71 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select add #11/B:1704@C2
85 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> select add #11/B:1301@O7
99 atoms, 99 bonds, 8 residues, 1 model selected
> select up
112 atoms, 113 bonds, 8 residues, 1 model selected
> color sel blue
> view matrix models
> #11,0.99985,-0.01723,-0.00013904,9.132,0.01723,0.99985,9.1223e-05,-1.2567,0.00013745,-9.3605e-05,1,5.9801
> select #11/A:802-824
177 atoms, 179 bonds, 23 residues, 1 model selected
> color sel yellow
> select #11/A:785-795
95 atoms, 96 bonds, 11 residues, 1 model selected
> select #11/A:785-802
144 atoms, 146 bonds, 18 residues, 1 model selected
> color sel orange
> select clear
> select #11/B
8651 atoms, 8873 bonds, 3 pseudobonds, 1089 residues, 2 models selected
> color (#!11 & sel) byhetero
> select clear
> show #!9 models
> show #!7 models
> show #!5 models
> show #!3 models
> show #!1 models
> cartoon style width 2.5 thickness 0.45
> select clear
[Repeated 1 time(s)]
> hide #!9 models
> hide #!7 models
> hide #!5 models
> hide #!3 models
> hide #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-4.cxs
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/SUST_data_collection/tr4-pp/atom
> selection from TR4_PP_20220615-coot-2.pdb"
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/SUST_data_collection/tr4-pp/postprocess_masked.mrc
Summary of feedback from opening
/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/SUST_data_collection/tr4-pp/atom
selection from TR4_PP_20220615-coot-2.pdb
---
warnings | Ignored bad PDB record found on line 98
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 99
BOND : 0.009 0.093 26679
Ignored bad PDB record found on line 100
ANGLE : 1.069 18.655 36456
Ignored bad PDB record found on line 101
CHIRALITY : 0.063 0.382 4359
Ignored bad PDB record found on line 102
PLANARITY : 0.008 0.084 4653
15 messages similar to the above omitted
Chain information for atom selection from TR4_PP_20220615-coot-2.pdb #13
---
Chain | Description
A B C | No description available
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.000838, step 1, values float32
> hide #!11 models
> volume #14 level 0.03311
> show #!2 models
> fitmap #14 inMap #2
Fit map postprocess_masked.mrc in map relion_locres_filtered-job083.mrc using
42671 points
correlation = 0.691, correlation about mean = 0.1059, overlap = 141.7
steps = 80, shift = 2.26, angle = 4.29 degrees
Position of postprocess_masked.mrc (#14) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99720199 -0.07475386 0.00023550 17.23470709
0.07475414 0.99720073 -0.00158631 -13.93100892
-0.00011626 0.00159947 0.99999871 1.53262547
Axis 0.02130354 0.00235223 0.99977029
Axis point 194.75689152 222.73109528 0.00000000
Rotation angle (degrees) 4.28807458
Shift along axis 1.86666472
> hide #!13 models
> fitmap #14 inMap #2
Fit map postprocess_masked.mrc in map relion_locres_filtered-job083.mrc using
42671 points
correlation = 0.6915, correlation about mean = 0.107, overlap = 141.7
steps = 44, shift = 0.0269, angle = 0.00715 degrees
Position of postprocess_masked.mrc (#14) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99719655 -0.07482629 0.00026998 17.24367121
0.07482661 0.99719544 -0.00149094 -13.96388745
-0.00015766 0.00150696 0.99999885 1.53383511
Axis 0.02002826 0.00285696 0.99979533
Axis point 195.03188600 222.65003359 0.00000000
Rotation angle (degrees) 4.29213093
Shift along axis 1.83898762
> select add #14
4 models selected
> view matrix models
> #14,0.9972,-0.074826,0.00026998,18.636,0.074827,0.9972,-0.0014909,-15.253,-0.00015766,0.001507,1,4.6177
> select subtract #14
Nothing selected
> fitmap #14 inMap #2
Fit map postprocess_masked.mrc in map relion_locres_filtered-job083.mrc using
42671 points
correlation = 0.9391, correlation about mean = 0.6978, overlap = 291.2
steps = 72, shift = 2.66, angle = 3.14 degrees
Position of postprocess_masked.mrc (#14) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99979748 -0.02012442 0.00010262 5.21506461
0.02012439 0.99979744 0.00027954 -3.28009811
-0.00010823 -0.00027741 0.99999996 6.77640951
Axis -0.01383613 0.00523805 0.99989056
Axis point 167.36917283 262.05390853 0.00000000
Rotation angle (degrees) 1.15324728
Shift along axis 6.68633026
> fitmap #13 inMap #14
Fit molecule atom selection from TR4_PP_20220615-coot-2.pdb (#13) to map
postprocess_masked.mrc (#14) using 26013 atoms
average map value = 0.02483, steps = 64
shifted from previous position = 2.02
rotated from previous position = 3.5 degrees
atoms outside contour = 17973, contour level = 0.033111
Position of atom selection from TR4_PP_20220615-coot-2.pdb (#13) relative to
postprocess_masked.mrc (#14) coordinates:
Matrix rotation and translation
0.99916256 -0.04089521 0.00132311 8.51040143
0.04089533 0.99916343 -0.00006432 -8.40842132
-0.00131937 0.00011838 0.99999912 -4.95315300
Axis 0.00223260 0.03229099 0.99947602
Axis point 205.67664701 204.17493156 0.00000000
Rotation angle (degrees) 2.34500951
Shift along axis -5.20307356
> show #!13 models
> hide #!2 models
> select add #13
26013 atoms, 26679 bonds, 6 pseudobonds, 3288 residues, 2 models selected
> view matrix models
> #13,0.99814,-0.060994,0.0014268,12.108,0.060994,0.99814,0.00024185,-11.234,-0.0014389,-0.00015438,1,5.5076
> view matrix models
> #13,0.99814,-0.060994,0.0014268,11.754,0.060994,0.99814,0.00024185,-11.377,-0.0014389,-0.00015438,1,7.1836
> select subtract #13
Nothing selected
> fitmap #13 inMap #14
Fit molecule atom selection from TR4_PP_20220615-coot-2.pdb (#13) to map
postprocess_masked.mrc (#14) using 26013 atoms
average map value = 0.07159, steps = 68
shifted from previous position = 2.15
rotated from previous position = 2.36 degrees
atoms outside contour = 3441, contour level = 0.033111
Position of atom selection from TR4_PP_20220615-coot-2.pdb (#13) relative to
postprocess_masked.mrc (#14) coordinates:
Matrix rotation and translation
0.99999996 0.00029104 -0.00005195 -0.04233567
-0.00029104 0.99999995 0.00007291 0.08333408
0.00005197 -0.00007290 1.00000000 -0.00598580
Axis -0.23942702 -0.17063346 -0.95580276
Axis point 287.27116391 144.15772950 0.00000000
Rotation angle (degrees) 0.01744650
Shift along axis 0.00163796
> fitmap #13 inMap #14
Fit molecule atom selection from TR4_PP_20220615-coot-2.pdb (#13) to map
postprocess_masked.mrc (#14) using 26013 atoms
average map value = 0.07159, steps = 44
shifted from previous position = 0.0183
rotated from previous position = 0.0183 degrees
atoms outside contour = 3427, contour level = 0.033111
Position of atom selection from TR4_PP_20220615-coot-2.pdb (#13) relative to
postprocess_masked.mrc (#14) coordinates:
Matrix rotation and translation
0.99999992 0.00030620 0.00026537 -0.12779117
-0.00030621 0.99999995 0.00003896 0.09620937
-0.00026536 -0.00003904 0.99999996 0.05191881
Axis -0.09580871 0.65188933 -0.75223733
Axis point 237.68690380 406.16853441 0.00000000
Rotation angle (degrees) 0.02332311
Shift along axis 0.03590610
> volume #14 level 0.03663
> volume #14 color #d6d6d6
> volume #14 color #d6d6d641
> volume #14 color #d6d6d625
> hide #!14 models
> show #!1 models
> select add #13
26013 atoms, 26679 bonds, 6 pseudobonds, 3288 residues, 2 models selected
> select add #1
51967 atoms, 53309 bonds, 18 pseudobonds, 6575 residues, 4 models selected
> cartoon style width 2.5 thickness 0.45
> cartoon style (#!1,13 & sel) xsection rectangle modeHelix default
> select clear
> hide pseudobonds
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #13/A/C
17342 atoms, 17785 bonds, 4 pseudobonds, 2192 residues, 2 models selected
> color (#!13 & sel) light gray
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-5.cxs
> select #13/B:14-290
2191 atoms, 2249 bonds, 276 residues, 1 model selected
> color sel blue
> select clear
> select #13/B:313-492
1436 atoms, 1478 bonds, 180 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #13/B:303-313,493-556
591 atoms, 602 bonds, 75 residues, 1 model selected
> color sel cyan
> select #13/B:291-302,557-659
794 atoms, 809 bonds, 1 pseudobond, 107 residues, 2 models selected
> color (#!13 & sel) forest green
> select #13/B:660-1100
3316 atoms, 3381 bonds, 1 pseudobond, 434 residues, 2 models selected
> color (#!13 & sel) red
> select clear
> select #13/C:794-816
151 atoms, 151 bonds, 21 residues, 1 model selected
> color sel yellow
> select #13/C:777-794
103 atoms, 104 bonds, 12 residues, 1 model selected
> color sel orange
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-6.cxs
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #13/B:1344@O6
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select up
58 atoms, 57 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #13/B:1338@C2
71 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
86 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 100 bonds, 7 residues, 1 model selected
> select add #13/B:1340@C2
99 atoms, 100 bonds, 8 residues, 1 model selected
> select up
112 atoms, 114 bonds, 8 residues, 1 model selected
> select up
114 atoms, 115 bonds, 9 residues, 1 model selected
> select up
126 atoms, 129 bonds, 9 residues, 1 model selected
> color sel red
> select #13/B:1330@C5
1 atom, 1 residue, 1 model selected
> select #13/C:716
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #13/B:1329@C7
1 atom, 1 residue, 1 model selected
> select #13/B:1329@O7
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
5144 atoms, 5290 bonds, 642 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #13/B:1329@O5
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #13/B:1322@O7
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
> select add #13/B:1327@O6
57 atoms, 56 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #13/B:1323@O6
71 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select add #13/B:1326@O6
85 atoms, 85 bonds, 7 residues, 1 model selected
> select up
98 atoms, 99 bonds, 7 residues, 1 model selected
> select add #13/B:1324@N2
99 atoms, 99 bonds, 8 residues, 1 model selected
> select up
112 atoms, 113 bonds, 8 residues, 1 model selected
> select add #13/B:1325@O3
113 atoms, 113 bonds, 9 residues, 1 model selected
> select up
126 atoms, 127 bonds, 9 residues, 1 model selected
> color sel blue
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #13/B:1334@C3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #13/B
8671 atoms, 8892 bonds, 2 pseudobonds, 1096 residues, 2 models selected
> color (#!13 & sel) byhetero
> view matrix models
> #13,0.9998,-0.019818,0.00036715,-1.4124,0.019818,0.9998,0.00032383,2.0155,-0.0003735,-0.00031649,1,12.509
> select clear
> show #!14 models
> fitmap #13 inMap #14
Fit molecule atom selection from TR4_PP_20220615-coot-2.pdb (#13) to map
postprocess_masked.mrc (#14) using 26013 atoms
average map value = 0.02407, steps = 76
shifted from previous position = 8.29
rotated from previous position = 2.05 degrees
atoms outside contour = 18978, contour level = 0.036632
Position of atom selection from TR4_PP_20220615-coot-2.pdb (#13) relative to
postprocess_masked.mrc (#14) coordinates:
Matrix rotation and translation
0.99935241 0.03595966 -0.00128665 -7.20367613
-0.03596132 0.99935236 -0.00128418 8.02471440
0.00123963 0.00132962 0.99999835 4.82269379
Axis 0.03629640 -0.03508100 -0.99872513
Axis point 214.34033816 198.77684135 0.00000000
Rotation angle (degrees) 2.06346038
Shift along axis -5.35952802
> select add #13
26013 atoms, 26679 bonds, 6 pseudobonds, 3288 residues, 2 models selected
> select add #14
26013 atoms, 26679 bonds, 6 pseudobonds, 3288 residues, 6 models selected
> fitmap #13 inMap #14
Fit molecule atom selection from TR4_PP_20220615-coot-2.pdb (#13) to map
postprocess_masked.mrc (#14) using 26013 atoms
average map value = 0.02403, steps = 64
shifted from previous position = 0.0338
rotated from previous position = 0.0106 degrees
atoms outside contour = 18979, contour level = 0.036632
Position of atom selection from TR4_PP_20220615-coot-2.pdb (#13) relative to
postprocess_masked.mrc (#14) coordinates:
Matrix rotation and translation
0.99935126 0.03599684 -0.00113446 -7.24751183
-0.03599818 0.99935115 -0.00118476 8.00790643
0.00109108 0.00122483 0.99999865 4.90897308
Axis 0.03343413 -0.03088036 -0.99896374
Axis point 214.21811958 200.18862508 0.00000000
Rotation angle (degrees) 2.06509180
Shift along axis -5.39348739
> select clear
> select add #14
4 models selected
> view matrix models
> #14,0.9998,-0.020124,0.00010262,5.1529,0.020124,0.9998,0.00027954,-3.2211,-0.00010823,-0.00027741,1,6.9824
> select subtract #14
Nothing selected
> select add #13
26013 atoms, 26679 bonds, 6 pseudobonds, 3288 residues, 2 models selected
> view matrix models
> #13,0.99987,0.015878,-0.0010078,-2.2145,-0.015879,0.99987,-0.00092781,4.6738,0.00099291,0.0009437,1,7.4956
> select clear
> fitmap #14 inMap #2
Fit map postprocess_masked.mrc in map relion_locres_filtered-job083.mrc using
39263 points
correlation = 0.9417, correlation about mean = 0.6874, overlap = 286
steps = 48, shift = 0.191, angle = 0.0073 degrees
Position of postprocess_masked.mrc (#14) relative to relion_locres_filtered-
job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99979541 -0.02022693 0.00003508 5.24941047
0.02022692 0.99979538 0.00024524 -3.29334165
-0.00004003 -0.00024448 0.99999997 6.78951035
Axis -0.01210471 0.00185669 0.99992501
Axis point 166.08556431 261.86710656 0.00000000
Rotation angle (degrees) 1.15908337
Shift along axis 6.71934391
> fitmap #13 inMap #2
Fit molecule atom selection from TR4_PP_20220615-coot-2.pdb (#13) to map
relion_locres_filtered-job083.mrc (#2) using 26013 atoms
average map value = 0.08677, steps = 68
shifted from previous position = 1.18
rotated from previous position = 2.04 degrees
atoms outside contour = 5330, contour level = 0.045245
Position of atom selection from TR4_PP_20220615-coot-2.pdb (#13) relative to
relion_locres_filtered-job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99980697 -0.01964657 0.00016005 5.08811776
0.01964655 0.99980698 0.00013106 -3.11564862
-0.00016260 -0.00012789 0.99999998 6.79429766
Axis -0.00658988 0.00821085 0.99994458
Axis point 163.95046312 259.63067248 0.00000000
Rotation angle (degrees) 1.12579990
Shift along axis 6.73480890
> hide #!14 models
> show #!1 models
> hide #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-6.cxs
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/1209_TR7_DTM_WJJ_maskupdate/atom
> selection from 20220622—RmYN02-add249NAG-coot-6-add—NAG-refined.pdb"
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/1209_TR7_DTM_WJJ_maskupdate/relion_locres_filtered.mrc
Chain information for atom selection from 20220622—RmYN02-add249NAG-
coot-6-add—NAG-refined.pdb #15
---
Chain | Description
A B C | No description available
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0244, step 1, values float32
> volume #16 level 0.05645
> hide #!13 models
> volume #16 level 0.07196
> volume #16 level 0.06679
> show #!2 models
> fitmap #16 inMap #2
Fit map relion_locres_filtered.mrc in map relion_locres_filtered-job083.mrc
using 59625 points
correlation = 0.7992, correlation about mean = 0.2649, overlap = 455.1
steps = 268, shift = 70.6, angle = 2.82 degrees
Position of relion_locres_filtered.mrc (#16) relative to
relion_locres_filtered-job083.mrc (#2) coordinates:
Matrix rotation and translation
0.99879044 0.04916633 0.00057189 34.01448910
-0.04916596 0.99879042 -0.00064304 50.85457821
-0.00060282 0.00061415 0.99999963 37.61505552
Axis 0.01278312 0.01194446 -0.99984695
Axis point 1059.84160668 -675.25859135 0.00000000
Rotation angle (degrees) 2.81858071
Shift along axis -36.56705670
> fitmap #15 inMap #16
Fit molecule atom selection from 20220622—RmYN02-add249NAG-coot-6-add—NAG-
refined.pdb (#15) to map relion_locres_filtered.mrc (#16) using 24423 atoms
average map value = 0.09548, steps = 336
shifted from previous position = 70.6
rotated from previous position = 2.82 degrees
atoms outside contour = 8051, contour level = 0.066789
Position of atom selection from 20220622—RmYN02-add249NAG-coot-6-add—NAG-
refined.pdb (#15) relative to relion_locres_filtered.mrc (#16) coordinates:
Matrix rotation and translation
0.99999993 0.00010988 -0.00035508 0.02529587
-0.00010991 0.99999999 -0.00007032 0.07904796
0.00035507 0.00007036 0.99999993 -0.07267215
Axis 0.18593704 -0.93863486 -0.29050304
Axis point 244.27100290 0.00000000 96.52789053
Rotation angle (degrees) 0.02167437
Shift along axis -0.04838226
> hide #!2 models
> hide #!16 models
> show #!1 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> select add #15
24423 atoms, 25035 bonds, 18 pseudobonds, 3087 residues, 2 models selected
> hide #!1 models
> hide #!15 models
> show #!15 models
> volume #16 color #d6d6d6
> volume #16 color #d6d6d626
> select subtract #15
Nothing selected
> select add #15
24423 atoms, 25035 bonds, 18 pseudobonds, 3087 residues, 2 models selected
> hide #!16 models
> color (#!15 & sel) light gray
> cartoon style (#!15 & sel) xsection rectangle modeHelix default
> hide pseudobonds
> show #!2 models
> hide #!2 models
> show #!1 models
> select clear
> select add #15
24423 atoms, 25035 bonds, 18 pseudobonds, 3087 residues, 2 models selected
> dssp
> cartoon style width 2.5 thickness 0.45
> select clear
> select #15/B:11-286
1835 atoms, 1883 bonds, 4 pseudobonds, 229 residues, 2 models selected
> color (#!15 & sel) blue
> select #15/B:309-488
1439 atoms, 1482 bonds, 180 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #15/B:299-309,489-552
599 atoms, 610 bonds, 75 residues, 1 model selected
> color sel cyan
> select #15/B:287-298,553-653
784 atoms, 799 bonds, 1 pseudobond, 107 residues, 2 models selected
> color (#!15 & sel) forest green
> select #15/B:654-1095
3197 atoms, 3259 bonds, 1 pseudobond, 418 residues, 2 models selected
> color (#!15 & sel) red
> select #15/A:788-810
37 atoms, 37 bonds, 4 residues, 1 model selected
> color sel yellow
> select #15/A:770-785
108 atoms, 109 bonds, 13 residues, 1 model selected
> color sel orange
> select clear
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #15/B:1301@C4
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 56 bonds, 4 residues, 1 model selected
Drag select of 1 residues
> select add #15/B:1294@C2
68 atoms, 56 bonds, 6 residues, 1 model selected
> select subtract #15/B:1294@C2
67 atoms, 56 bonds, 5 residues, 1 model selected
> select up
69 atoms, 68 bonds, 6 residues, 1 model selected
> select up
81 atoms, 81 bonds, 6 residues, 1 model selected
> select add #15/B:1303@O6
82 atoms, 81 bonds, 7 residues, 1 model selected
> select up
95 atoms, 95 bonds, 7 residues, 1 model selected
> select up
97 atoms, 96 bonds, 8 residues, 1 model selected
> select up
109 atoms, 109 bonds, 8 residues, 1 model selected
> color sel blue
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #15/B:1298@C3
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add #15/B:1298@C8
30 atoms, 28 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel forest green
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #15/B:1296@C5
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select add #15/B:1300@C2
43 atoms, 42 bonds, 4 residues, 1 model selected
> select up
45 atoms, 44 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #15/B:1299@C4
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select add #15/B:1291@C2
29 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select add #15/B:1308@N2
43 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 72 bonds, 5 residues, 1 model selected
> select add #15/B:1285@C5
71 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 86 bonds, 6 residues, 1 model selected
> select up
86 atoms, 87 bonds, 7 residues, 1 model selected
> select up
98 atoms, 100 bonds, 7 residues, 1 model selected
> color sel red
> select #15/B:
Expected an objects specifier or a keyword
> select #15/B
8141 atoms, 8345 bonds, 6 pseudobonds, 1029 residues, 2 models selected
> color (#!15 & sel) byhetero
> select clear
> show #!16 models
> hide #!16 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-7.cxs
> includeMaps true
> show #!13 models
> hide #!13 models
> show #!16 models
> hide #!16 models
> ui tool show "Side View"
> show #!13 models
> hide #!15 models
> show #!11 models
> hide #!13 models
> show #!13 models
> hide #!11 models
> select #13/B:422
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #13/B:1332@O6
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel byhetero
> select clear
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!13 models
> show #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/FIg2-1122/1122-7.cxs
> includeMaps true
——— End of log from Wed Nov 22 19:27:48 2023 ———
opened ChimeraX session
> show #!7 models
> select #7/B:809-821
107 atoms, 108 bonds, 13 residues, 1 model selected
> color sel orange
> select clear
> select #7/B:826-848
169 atoms, 170 bonds, 22 residues, 1 model selected
> color sel yellow
> select clear
> hide #!1 models
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/banal-20-236.png
> width 2030 height 1210 supersample 4 transparentBackground true
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/laos-20-236.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!15 models
> hide #!7 models
> show #!7 models
> hide #!15 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/1205.cxs"
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/laos-20-236.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!9 models
> hide #!7 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/tr5_GX2013.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!11 models
> hide #!9 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/HeB2013.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!13 models
> hide #!11 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/YN2013_PP.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!15 models
> hide #!13 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/RmYN02.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!5 models
> hide #!15 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/laos-20-52.png" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!3 models
> hide #!5 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BtKY72.png" width 1926 height 1340 supersample 4
> transparentBackground true
[Repeated 1 time(s)]
> show #!1 models
> hide #!3 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BM48-31.png" width 1926 height 1340 supersample 4
> transparentBackground true
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/20211017_TR2_DTM/20231205_TR2_DTM-
> coot-4—remove670and671_add_BLA_phenix.pdb
Chain information for 20231205_TR2_DTM-
coot-4—remove670and671_add_BLA_phenix.pdb #17
---
Chain | Description
A B C | No description available
> mmaker #17 to #3 showAlignment true
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 atom selection from Kenya_TR2_DTM-coot-3-20231113.pdb, chain A (#3)
with 20231205_TR2_DTM-coot-4—remove670and671_add_BLA_phenix.pdb, chain A
(#17), sequence alignment score = 5425.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: atom selection from
Kenya_TR2_DTM-coot-3-20231113.pdb #3/A, 20231205_TR2_DTM-
coot-4—remove670and671_add_BLA_phenix.pdb #17/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 1084 pruned atom pairs is 0.229 angstroms; (across all 1092
pairs: 0.398)
> show #!3 models
> hide #!1 models
> select add #17
26617 atoms, 27328 bonds, 6 pseudobonds, 3349 residues, 2 models selected
> dssp
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide pesduo
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select add #17
26617 atoms, 27328 bonds, 6 pseudobonds, 3349 residues, 2 models selected
> hide #!3 models
> cartoon style (#!17 & sel) xsection oval modeHelix default
> cartoon style (#!17 & sel) xsection rectangle modeHelix default
> select clear
> select add #17
26617 atoms, 27328 bonds, 6 pseudobonds, 3349 residues, 2 models selected
> color (#!17 & sel) light gray
> show #!3 models
> select clear
> select #17/A:17-297
2246 atoms, 2313 bonds, 281 residues, 1 model selected
> color sel blue
> select #17/A: 320-517
1546 atoms, 1594 bonds, 198 residues, 1 model selected
> color sel cornflower blue
> select #17/A: 310-320,518-581
590 atoms, 603 bonds, 75 residues, 1 model selected
> color sel cyan
> select #17/A: 298-309,582-684
854 atoms, 870 bonds, 1 pseudobond, 113 residues, 2 models selected
> color (#!17 & sel) forest green
> select #17/A: 685-1126
3282 atoms, 3344 bonds, 1 pseudobond, 426 residues, 2 models selected
> color (#!17 & sel) red
> select clear
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #17/A:888
19 atoms, 18 bonds, 2 residues, 1 model selected
> select up
21 atoms, 19 bonds, 3 residues, 1 model selected
> select up
33 atoms, 32 bonds, 3 residues, 1 model selected
> select up
35 atoms, 33 bonds, 4 residues, 1 model selected
> select up
47 atoms, 46 bonds, 4 residues, 1 model selected
> select up
49 atoms, 47 bonds, 5 residues, 1 model selected
> select up
61 atoms, 60 bonds, 5 residues, 1 model selected
> color sel red
> color sel byhetero
> select clear
> select #17/A:1142@C8
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #17/A:1140@C3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel forest green
> color sel byhetero
> select clear
> select #17/B: 819-841
88 atoms, 88 bonds, 11 residues, 1 model selected
> color sel yellow
> select clear
> select #17/B: 803-820
99 atoms, 99 bonds, 12 residues, 1 model selected
> color sel orange
> select clear
> select #17/A:1128@C7
1 atom, 1 residue, 1 model selected
> select #17/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #17/A:1131@C8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select up
44 atoms, 44 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select add #17/A:1135@O5
71 atoms, 71 bonds, 6 residues, 1 model selected
> select add #17/A:1135@C5
72 atoms, 71 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
5389 atoms, 5556 bonds, 672 residues, 1 model selected
> select down
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
86 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 100 bonds, 7 residues, 1 model selected
> select up
100 atoms, 101 bonds, 8 residues, 1 model selected
> select up
109 atoms, 112 bonds, 8 residues, 1 model selected
> select down
109 atoms, 113 bonds, 8 residues, 1 model selected
> select up
113 atoms, 114 bonds, 10 residues, 1 model selected
> select up
130 atoms, 134 bonds, 10 residues, 1 model selected
> select up
132 atoms, 135 bonds, 11 residues, 1 model selected
> select up
141 atoms, 146 bonds, 11 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
> select #17/C:412
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #17/C:447@NE2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel light gray
> select clear
> select #17/A:1127@C7
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BtKY72-new.png" width 1926 height 1340 supersample 4
> transparentBackground true
> select #17/A:320-517
1546 atoms, 1594 bonds, 198 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select #17/A:1139@O6
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/A:1139@O7
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add #17/A:1127@O3
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #17/A:371
40 atoms, 40 bonds, 3 residues, 1 model selected
> select up
42 atoms, 41 bonds, 4 residues, 1 model selected
> select add #17/A:1127@C4
43 atoms, 41 bonds, 4 residues, 1 model selected
> select up
54 atoms, 54 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel royal blue
> color sel byhetero
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BtKY72-new-1.png" width 1926 height 1340 supersample 4
> transparentBackground true
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/1205.cxs" includeMaps true
> select add #17
26617 atoms, 27328 bonds, 6 pseudobonds, 3349 residues, 2 models selected
> cartoon style width 2.5 thickness 0.45
> select clear
> show #!16 models
> hide #!16 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BtkY72_thickCartoon.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> ui tool show "Side View"
> select clear
> select #17/A:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select add #17/A:1151@CAB
29 atoms, 28 bonds, 3 residues, 1 model selected
> select up
71 atoms, 74 bonds, 3 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BtkY72_thickCartoon.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!15 models
> hide #!17 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/RmYN02.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!13 models
> hide #!15 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/TR4_PP.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!11 models
> hide #!13 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/HeB2013.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!9 models
> hide #!11 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/GX2013_tr5.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!7 models
> hide #!9 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/20-236.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> show #!5 models
> hide #!7 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/20-52.tif" width 1926 height 1340 supersample 4 transparentBackground
> true
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!5 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/BM48-31-1.tif" width 1926 height 1340 supersample 4
> transparentBackground true
> lighting full
> lighting soft
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting full
> lighting simple
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/BM48-31-1.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!17 models
> hide #!1 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/BtkY72_thickCartoon.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!13 models
> hide #!17 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/TR4_PP.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!9 models
> hide #!13 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/GX2013_tr5.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!11 models
> hide #!9 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/HeB2013.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!15 models
> hide #!11 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/RmYN02.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!7 models
> hide #!15 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/20-236.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!5 models
> hide #!7 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/20-52.tif" width 2018 height 1340 supersample 4
> transparentBackground true
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/overview.cxs" includeMaps true
——— End of log from Tue Dec 5 20:42:09 2023 ———
opened ChimeraX session
> show #!17 models
> hide #!5 models
> select #17/A:1150
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #17/A: 1150
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #17/A: 1151
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel purple
> color sel magenta
> color sel purple
> color sel byhetero
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/tr2.png" width 2018 height 1340 supersample 4
> transparentBackground true
[Repeated 1 time(s)]
> show #!15 models
> hide #!17 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/tr7.png" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!13 models
> hide #!15 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/tr4_PP.png" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!11 models
> hide #!13 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/tr6.png" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!9 models
> hide #!11 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/tr5.png" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!7 models
> hide #!9 models
> select add #7
26337 atoms, 26941 bonds, 12 pseudobonds, 3333 residues, 2 models selected
> dssp
> select clear
> select add #7
26337 atoms, 26941 bonds, 12 pseudobonds, 3333 residues, 2 models selected
> cartoon style (#!7 & sel) xsection oval modeHelix default
> select clear
> select add #7
26337 atoms, 26941 bonds, 12 pseudobonds, 3333 residues, 2 models selected
> cartoon style (#!7 & sel) xsection rectangle modeHelix default
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/20-236-12-5.png" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!5 models
> hide #!7 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/20-52-12-5.png" width 2018 height 1340 supersample 4
> transparentBackground true
> show #!1 models
> hide #!5 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/BM48-31.png" width 2018 height 1340 supersample 4
> transparentBackground true
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/overview.cxs"
> open
> "/Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/LAOS-20-52-SUST/CryoSPARC/Copy_of_atom
> selection from
> laos_20-52_fittedSUST_300kv_coot_0-coot-2_real_space_refined.pdb"
Chain information for Copy_of_atom selection from
laos_20-52_fittedSUST_300kv_coot_0-coot-2_real_space_refined.pdb #18
---
Chain | Description
A B C | No description available
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2021_Experiment_Rawdata/EM_data_Processing/laos_20_52_EM_data/LAOS-20-52-SUST/CryoSPARC/refinement/cryosparc_P154_J13_004_volume_map.mrc
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.127, step 2, values float32
> volume #19 step 1
> volume #19 level 0.5504
> show #!2 models
> hide #!2 models
> ui mousemode right rotate
> select add #19
4 models selected
> ui mousemode right "translate selected models"
> view matrix models #19,1,0,0,0.33567,0,1,0,-0.43881,0,0,1,-2.4051
> view matrix models #19,1,0,0,-14.378,0,1,0,2.5934,0,0,1,-39.321
> view matrix models #19,1,0,0,-33.886,0,1,0,11.943,0,0,1,-41.444
> view matrix models #19,1,0,0,-21.784,0,1,0,8.8661,0,0,1,-16.205
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.13775,0.31714,-0.93832,289.9,0.51991,0.78319,0.34103,-123.98,0.84304,-0.53482,-0.057,162.99
> view matrix models
> #19,0.29857,0.39168,-0.87031,226.26,0.63371,0.60051,0.48766,-139.51,0.71363,-0.69712,-0.068918,227.02
> view matrix models
> #19,0.71772,0.14339,-0.68141,154.1,0.6939,-0.22899,0.68269,-14.203,-0.058147,-0.96281,-0.26385,483.41
> view matrix models
> #19,-0.018273,0.30114,-0.9534,328.17,0.99067,0.13428,0.023428,-7.8058,0.13508,-0.94408,-0.30078,448.51
> view matrix models
> #19,-0.60431,0.062767,-0.79428,463.14,0.47907,0.82518,-0.29928,16.212,0.63664,-0.56137,-0.52873,314.34
> view matrix models
> #19,-0.84512,0.4921,-0.20884,289.33,0.50506,0.60695,-0.61362,127.7,-0.1752,-0.62405,-0.76148,542.99
> view matrix models
> #19,-0.91198,0.40654,0.054856,263.33,0.38273,0.89135,-0.24293,8.8345,-0.14766,-0.20055,-0.96849,490.94
> view matrix models
> #19,-0.83272,0.54776,-0.080873,246.53,0.52846,0.74264,-0.41135,48.897,-0.16526,-0.38528,-0.90788,521.31
> view matrix models
> #19,-0.56319,0.80381,-0.19159,160.88,0.79983,0.47204,-0.37074,44.074,-0.20757,-0.36204,-0.90876,524.98
> view matrix models
> #19,-0.67949,0.71576,-0.16118,196.78,0.70208,0.57056,-0.42609,54.556,-0.21302,-0.40268,-0.89021,530.84
> view matrix models
> #19,-0.73254,0.66192,-0.15892,218.69,0.64177,0.59368,-0.48547,74.774,-0.22699,-0.45761,-0.85969,538.88
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.73254,0.66192,-0.15892,238.96,0.64177,0.59368,-0.48547,65.049,-0.22699,-0.45761,-0.85969,540.97
> view matrix models
> #19,-0.73254,0.66192,-0.15892,237.6,0.64177,0.59368,-0.48547,65.792,-0.22699,-0.45761,-0.85969,541.64
> select subtract #19
Nothing selected
> ui mousemode right select
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #19 inMap #2
Fit map cryosparc_P154_J13_004_volume_map.mrc in map relion_locres_filtered-
job083.mrc using 102021 points
correlation = 0.9413, correlation about mean = 0.6479, overlap = 7819
steps = 196, shift = 26.7, angle = 31 degrees
Position of cryosparc_P154_J13_004_volume_map.mrc (#19) relative to
relion_locres_filtered-job083.mrc (#2) coordinates:
Matrix rotation and translation
-0.66045223 0.75086806 0.00002210 192.18929080
0.75086806 0.66045223 -0.00005191 -85.51462624
-0.00005357 -0.00001769 -1.00000000 418.34950412
Axis 0.41203889 0.91116626 -0.00001928
Axis point 115.43471462 0.00000000 209.17166378
Rotation angle (degrees) 179.99762090
Shift along axis 1.26335466
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> mmaker #18 to #5 showAlignment true
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 Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-
coot-3-20230529.pdb, chain C (#5) with Copy_of_atom selection from
laos_20-52_fittedSUST_300kv_coot_0-coot-2_real_space_refined.pdb, chain A
(#18), sequence alignment score = 5466.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
Laos-20-52_20220721ddNAGS—beforePhenix_real_space_refined-coot-3-20230529.pdb
#5/C, Copy_of_atom selection from
laos_20-52_fittedSUST_300kv_coot_0-coot-2_real_space_refined.pdb #18/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 1068 pruned atom pairs is 0.916 angstroms; (across all 1106
pairs: 1.064)
> hide #!1 models
> hide #!19 models
> show #!5 models
> hide #!5 models
> select add #18
27180 atoms, 27898 bonds, 9 pseudobonds, 3399 residues, 2 models selected
> cartoon style (#!18 & sel) xsection rectangle modeHelix default
> color (#!18 & sel) light gray
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> cartoon style width 2.5 thickness 0.45
> select clear
[Repeated 2 time(s)]
Mismatch between Cocoa '\x0' and Carbon 'd' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'D' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'd' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'D' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2202' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ce' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2202' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ce' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x4' for virtual key 2 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> dssp
> select add #18
27180 atoms, 27898 bonds, 9 pseudobonds, 3399 residues, 2 models selected
> dssp
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel purple
> color sel byhetero
> select clear
> select #18/A:13-307
2331 atoms, 2400 bonds, 1 pseudobond, 288 residues, 2 models selected
> color (#!18 & sel) blue
> select clear
> select #18/A:330-528
1571 atoms, 1618 bonds, 199 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select #18/A:320-330, 529-592
589 atoms, 600 bonds, 75 residues, 1 model selected
> color sel cyan
> select #18/A:308-319,593-695
802 atoms, 817 bonds, 1 pseudobond, 107 residues, 2 models selected
> color (#!18 & sel) forest green
> select clear
> select #18/A:696-1136
3361 atoms, 3426 bonds, 1 pseudobond, 438 residues, 2 models selected
> color (#!18 & sel) red
> select clear
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #18/C:830-852
177 atoms, 179 bonds, 23 residues, 1 model selected
> color sel yellow
> select #18/C:803-820
147 atoms, 151 bonds, 18 residues, 1 model selected
> color sel orange
> select clear
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
5413 atoms, 5574 bonds, 672 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
42 atoms, 42 bonds, 3 residues, 1 model selected
> select up
44 atoms, 43 bonds, 4 residues, 1 model selected
> select up
56 atoms, 57 bonds, 4 residues, 1 model selected
> select up
58 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> select up
72 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
5413 atoms, 5574 bonds, 672 residues, 1 model selected
> select down
84 atoms, 85 bonds, 6 residues, 1 model selected
> select up
86 atoms, 86 bonds, 7 residues, 1 model selected
> select up
98 atoms, 100 bonds, 7 residues, 1 model selected
> select add #18/A:1317@C4
99 atoms, 100 bonds, 8 residues, 1 model selected
> select add #18/A:1317@O4
100 atoms, 100 bonds, 8 residues, 1 model selected
> select up
112 atoms, 114 bonds, 8 residues, 1 model selected
> select up
114 atoms, 115 bonds, 9 residues, 1 model selected
> select up
126 atoms, 128 bonds, 9 residues, 1 model selected
> color sel blue
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel forest green
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel byhetero
> color sel cornflower blue
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
30 atoms, 30 bonds, 3 residues, 1 model selected
> select up
42 atoms, 43 bonds, 3 residues, 1 model selected
> select up
44 atoms, 44 bonds, 4 residues, 1 model selected
> select up
56 atoms, 58 bonds, 4 residues, 1 model selected
> select add #18/A:1316@C2
57 atoms, 58 bonds, 5 residues, 1 model selected
> select up
70 atoms, 72 bonds, 5 residues, 1 model selected
> select add #18/A:1315@O3
71 atoms, 72 bonds, 6 residues, 1 model selected
> select up
84 atoms, 87 bonds, 6 residues, 1 model selected
> select up
86 atoms, 88 bonds, 7 residues, 1 model selected
> select up
98 atoms, 101 bonds, 7 residues, 1 model selected
> select add #18/A:899
103 atoms, 105 bonds, 8 residues, 1 model selected
> select up
190 atoms, 195 bonds, 18 residues, 1 model selected
> select add #18/A:1312@O3
191 atoms, 195 bonds, 19 residues, 1 model selected
> select up
204 atoms, 209 bonds, 19 residues, 1 model selected
> color sel red
> color sel byhetero
> select clear
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'H' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'H' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02d9' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u534a' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02d9' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u534a' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select add #18
27180 atoms, 27898 bonds, 9 pseudobonds, 3399 residues, 2 models selected
> hide speudo
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/20-52-1205-new.png" width 2018 height 1340 supersample 4
> transparentBackground true
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/1205-overview.cxs"
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/1205-overview.cxs" includeMaps true
——— End of log from Tue Dec 5 22:13:05 2023 ———
opened ChimeraX session
> volume #19 level 0.5122
> transparency #18-19 80
> select #18/A:1899@O7
1 atom, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #18/A:281@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #18/A:1397@C8
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> ui tool show "Side View"
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/laos-20-52.png" width 1990 height 1340 supersample 4
> transparentBackground true
[Repeated 1 time(s)]
> ui tool show "Model Panel"
> show #!17 models
> hide #!18 models
> hide #!19 models
> show #!4 models
> select add #4
2 models selected
> color #4.1 dark gray
> transparency #4.1 90
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/BtKY72.png" width 1990 height 1340 supersample 4
> transparentBackground true
> show #!1 models
> show #!2 models
> hide #!4 models
> hide #!17 models
> select add #1
25954 atoms, 26630 bonds, 12 pseudobonds, 3287 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
4 models selected
> color #2.1 dark gray
> transparency #2.1 90
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/BM48-31.png" width 1990 height 1340 supersample 4
> transparentBackground true
> show #!13 models
> show #!14 models
> hide #!2 models
> hide #!1 models
> select add #14
4 models selected
> color #14.1 dark gray
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/tr4_PP.png" width 1990 height 1340 supersample 4
> transparentBackground true
> hide #!14 models
> show #!2 models
> hide #!2 models
> show #!9 models
> show #!10 models
> hide #!13 models
> select add #10
4 models selected
> transparency #10.1 90
> select clear
> select add #10
4 models selected
> transparency #10.1 90
> select add #9
25312 atoms, 25883 bonds, 15 pseudobonds, 3187 residues, 6 models selected
> cartoon style (#!9 & sel) xsection rectangle modeHelix default
> select clear
> hide #!10 models
> select #9/C:604@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!8 models
> hide #!8 models
> show #!10 models
> volume #10 level 0.03399
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/DomainD-C.cxs" includeMaps true
——— End of log from Wed Dec 6 10:01:17 2023 ———
opened ChimeraX session
> ui tool show "Model Panel"
> select #9/C:1301@O3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
362 atoms, 372 bonds, 42 residues, 1 model selected
> select down
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #9/C:1310@O4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #10
14 atoms, 14 bonds, 1 residue, 5 models selected
> select add #9
25312 atoms, 25883 bonds, 15 pseudobonds, 3187 residues, 6 models selected
> select subtract #9
4 models selected
> color #10.1 gray
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/GX2013.png" width 1990 height 1340 supersample 4
> transparentBackground true
> select #9/C:630@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/GX2013.png" width 2088 height 1340 supersample 4
> transparentBackground true
> show #!11 models
> show #!12 models
> hide #!9 models
> hide #!10 models
> ui tool show "Fit in Map"
> fitmap #11 inMap #12
Fit molecule HeB2013_20230620_edit_add360N.pdb (#11) to map postprocess.mrc
(#12) using 25953 atoms
average map value = 0.01775, steps = 108
shifted from previous position = 5.25
rotated from previous position = 3.42 degrees
atoms outside contour = 19422, contour level = 0.028219
Position of HeB2013_20230620_edit_add360N.pdb (#11) relative to
postprocess.mrc (#12) coordinates:
Matrix rotation and translation
0.99820595 0.05961939 -0.00551526 -11.16980655
-0.05962613 0.99822021 -0.00106647 13.21602228
0.00544186 0.00139341 0.99998422 3.78739561
Axis 0.02053781 -0.09148235 -0.99559489
Axis point 207.93044359 191.81446323 0.00000000
Rotation angle (degrees) 3.43330172
Shift along axis -5.20914777
> select add #11
25953 atoms, 26619 bonds, 9 pseudobonds, 3267 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.9949,0.038326,0.093321,-23.557,-0.035875,0.99897,-0.027799,14.092,-0.09429,0.024309,0.99525,22.441
> view matrix models
> #11,0.99684,0.072981,0.031464,-19.775,-0.061499,0.95911,-0.27627,74.157,-0.050339,0.27346,0.96057,-33.008
> view matrix models
> #11,0.99578,0.087602,0.027228,-21.896,-0.076554,0.95708,-0.27952,78.187,-0.050546,0.27626,0.95975,-33.413
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.99578,0.087602,0.027228,-20.523,-0.076554,0.95708,-0.27952,77.744,-0.050546,0.27626,0.95975,-32.069
> view matrix models
> #11,0.99578,0.087602,0.027228,-20.63,-0.076554,0.95708,-0.27952,77.875,-0.050546,0.27626,0.95975,-34.024
> ui mousemode right "move picked models"
> view matrix models
> #12,0.99985,-0.017418,0.00016392,3.7169,0.017418,0.99985,-7.0431e-05,-2.3503,-0.00016267,7.3275e-05,1,1.6294
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.995,0.092913,0.036585,-23.359,-0.080897,0.96482,-0.25016,71.594,-0.058541,0.24595,0.96751,-27.415
> ui mousemode right select
> fitmap #11 inMap #12
Fit molecule HeB2013_20230620_edit_add360N.pdb (#11) to map postprocess.mrc
(#12) using 25953 atoms
average map value = 0.04561, steps = 128
shifted from previous position = 7.12
rotated from previous position = 15.9 degrees
atoms outside contour = 6187, contour level = 0.028219
Position of HeB2013_20230620_edit_add360N.pdb (#11) relative to
postprocess.mrc (#12) coordinates:
Matrix rotation and translation
0.99999998 0.00019130 -0.00011401 -0.04476942
-0.00019127 0.99999993 0.00032596 -0.02952102
0.00011407 -0.00032593 0.99999994 0.04824329
Axis -0.82567777 -0.28888458 -0.48456364
Axis point 0.00000000 180.88294810 71.00623162
Rotation angle (degrees) 0.02261808
Shift along axis 0.02211634
> select clear
> color #11-12 gray
> undo
> select add #11
25953 atoms, 26619 bonds, 9 pseudobonds, 3267 residues, 2 models selected
> select add #12
25953 atoms, 26619 bonds, 9 pseudobonds, 3267 residues, 6 models selected
> select subtract #11
4 models selected
> transparency #12.1 80
> select clear
> select #12
4 models selected
> select #12
4 models selected
> select clear
[Repeated 1 time(s)]
> hide #!12 models
> select #11/B:603@CB
1 atom, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #11/B:603@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!12 models
> select #11/B:591@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #11/B:1309@C8
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #11/B:629@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/HeB2013.png" width 1882 height 1340 supersample 4
> transparentBackground true
> show #!13 models
> show #!14 models
> hide #!12 models
> hide #!11 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/tr4_PP.png" width 1882 height 1340 supersample 4
> transparentBackground true
> show #!15 models
> show #!16 models
> hide #!14 models
> hide #!13 models
> select add #16
4 models selected
> color #16.1 gray
> select clear
> volume #16 level 0.05542
> volume #16 level 0.08126
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/RmYN02.png" width 1882 height 1340 supersample 4
> transparentBackground true
> show #!8 models
> show #!7 models
> hide #!15 models
> hide #!16 models
> volume #8 level 0.02557
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
4167 atoms, 4281 bonds, 526 residues, 1 model selected
> select up
4330 atoms, 4449 bonds, 545 residues, 1 model selected
> select up
5861 atoms, 6009 bonds, 740 residues, 1 model selected
> select up
5995 atoms, 6142 bonds, 758 residues, 1 model selected
> hide #!8 models
> select up
8737 atoms, 8948 bonds, 1108 residues, 1 model selected
> select clear
> select #7/A:653@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!8 models
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/laos-20-236.png" width 1882 height 1340 supersample
> 4 transparentBackground true
> show #!1 models
> show #!2 models
> hide #!7 models
> hide #!8 models
> select add #2
4 models selected
> color #2.1 gray
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/BM48-31.png" width 1882 height 1340 supersample 4
> transparentBackground true
> show #!19 models
> show #!18 models
> hide #!2 models
> hide #!1 models
> select add #19
4 models selected
> color #19.1 gray
> select clear
> hide #!19 models
> show #!19 models
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/laos-20-52.png" width 1882 height 1340 supersample 4
> transparentBackground true
> show #!17 models
> hide #!18 models
> hide #!19 models
> show #!4 models
> select add #4
2 models selected
> color #4.1 gray
> select clear
> select #17/A:1142@C8
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #17/A:648@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/BtKY72.png" width 1882 height 1340 supersample 4
> transparentBackground true
> save "/Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/New
> Folder/未命名文件夹/DomainD-C/DomainD-C.cxs"
——— End of log from Wed Dec 6 10:34:57 2023 ———
opened ChimeraX session
> ui tool show "Model Panel"
> show #!13 models
> show #!14 models
> hide #!17 models
> hide #!4 models
> volume #14 color #a9a9a94d
> ui tool show "Side View"
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/DomainD-
> FPPR.cxs
——— End of log from Fri Jun 7 23:53:06 2024 ———
opened ChimeraX session
> volume #14 level 0.0359
> ui tool show "Hide Dust"
> surface dust #14 size 5.6
> surface dust #14 size 5.89
> surface dust #14 size 2.63
> surface dust #14 size 2.46
> surface dust #14 size 2.38
> surface dust #14 size 2.3
> surface dust #14 size 3.56
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/YN2013-tr4-DomainD-
> FPPR.cxs
——— End of log from Fri Jun 7 23:56:04 2024 ———
opened ChimeraX session
> ui tool show "Model Panel"
> show #!9 models
> show #!10 models
> hide #!14 models
> hide #!13 models
> volume #10 color #80808052
> volume #10 color #8080804c
> ui tool show "Hide Dust"
> surface dust #10 size 7.92
> volume #10 level 0.03087
> ui tool show "Side View"
> select #9/C:65@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/GX2013-DOmainD-
> FPPR.cxs
> show #!11 models
> show #!12 models
> hide #!9 models
> hide #!10 models
> volume #12 color #d6d6d64e
> volume #12 color #d6d6d64d
> volume #12 color silver
> volume #12 color darkgrey
> volume #12 color silver
> volume #12 color #c0c0c064
> volume #12 color #c0c0c04f
> volume #12 color #c0c0c04c
> ui tool show "Hide Dust"
> surface dust #10 size 7.92
[Repeated 1 time(s)]
> surface dust #10 size 7.33
> surface dust #10 size 6.41
[Repeated 2 time(s)]
> surface dust #10 size 6.09
> surface dust #10 size 7.84
> surface dust #12 size 9.86
> volume #12 level 0.02145
> ui tool show "Side View"
[Repeated 2 time(s)]
> select clear
> select #11/B:1703@O7
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
398 atoms, 409 bonds, 46 residues, 1 model selected
> hide sel atoms
> select clear
> save
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/HeB2013-DOmainD-
> FPPR.cxs
——— End of log from Sat Jun 8 00:54:17 2024 ———
opened ChimeraX session
> open
> /Users/Jingjing/Documents/2021_GuangZHou/2023/ChimeraX/Fig2-1122/20240607-edit/HeB2013-DOmainD-
> FPPR_changedFPPR_update.cxs
Opened relion_locres_filtered-job083.mrc as #2, grid size 256,256,256, pixel
1.65, shown at level 0.0452, step 1, values float32
Opened tr2_dtm_postprocess.mrc as #4, grid size 256,256,256, pixel 1.64, shown
at level 0.0217, step 1, values float32
Opened postprocess.mrc as #6, grid size 256,256,256, pixel 1.32, shown at
level 0.0259, step 1, values float32
Opened laos_20_236_job019_postprocess.mrc as #8, grid size 256,256,256, pixel
1.32, shown at level 0.0256, step 1, values float32
Opened postprocess.mrc as #10, grid size 240,240,240, pixel 1.32, shown at
level 0.0309, step 1, values float32
Opened postprocess.mrc as #12, grid size 256,256,256, pixel 1.64, shown at
level 0.0214, step 1, values float32
Opened postprocess_masked.mrc as #14, grid size 256,256,256, pixel 1.64, shown
at level 0.0359, step 1, values float32
Opened relion_locres_filtered.mrc as #16, grid size 256,256,256, pixel 1.32,
shown at level 0.0813, step 1, values float32
Opened cryosparc_P154_J13_004_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.17, shown at level 0.512, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 757, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1215, in restore_snapshot
sseq = StructureSeq(chain_id=data['chain_id'], structure=data['structure'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1060, in __init__
chain_id.encode('utf-8'), structure._c_pointer, polymer_type)
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute '_c_pointer'
Exception ignored in: <function StructureSeq.__del__ at 0x289bcc400>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1075, in __del__
self.changes_handler.remove()
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'changes_handler'
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX73CH/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D56)
Kernel Version: Darwin 23.3.0
Time since boot: 2 days, 6 hours, 18 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL D2421DS:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56.1
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202404160016
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.0
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Milestone: | → 1.8 |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → "Demoted" StructureSeq does not save/restore correctly |
comment:2 by , 17 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Fix: https://github.com/RBVI/ChimeraX/commit/cdc1704ac5cb099af3452e43d9d13765135f3087