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Opened 14 months ago
Closed 14 months ago
#15774 closed defect (limitation)
MemoryError saving map in session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/yulab/Desktop/DS1-session/session 8-2024.7.26.cxs"
Opened long_full_spike_230505_reconstruction.mrc as #2, grid size 288,288,288,
pixel 1.06, shown at level 0.00465, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc as #4, grid size
288,288,288, pixel 1.06, shown at level 0.0226, step 1, values float32
Opened empty_spike_230505_reconstruction.mrc as #15, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
Opened DS1_NTR_C_long_spike_reconstruction.mrc as #13.1, grid size
300,300,300, pixel 1.06, shown at level 0.0051, step 2, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc as #13.2, grid size
300,300,300, pixel 1.06, shown at level 0.0177, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc as #13.3, grid size
300,300,300, pixel 1.06, shown at level 0.0189, step 2, values float32
Opened DS1_NTR_C_long_spike_reconstruction.mrc as #5.1, grid size 300,300,300,
pixel 1.06, shown at level 0.0193, step 2, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc as #5.2, grid size
300,300,300, pixel 1.06, shown at level 0.0177, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc as #5.3, grid size
300,300,300, pixel 1.06, shown at level 0.0189, step 2, values float32
Opened long_full_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at level 0.00255, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at level 0.00248, step 1, values float32
Opened empty_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at level 0.00244, step 1, values float32
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at level 0.00224, step 1, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at level 0.00223, step 1, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc gaussian as #11, grid size
300,300,300, pixel 1.06, shown at level 0.00216, step 1, values float32
Log from Fri Jul 26 19:57:23 2024UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/yulab/Desktop/session 5-2024.7.25.cxs"
Opened long_full_spike_230505_reconstruction.mrc as #2, grid size 288,288,288,
pixel 1.06, shown at level 0.00465, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc as #4, grid size
288,288,288, pixel 1.06, shown at level 0.0226, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at level 0.00084, step 1, values float32
Opened long_full_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at level 0.00297, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at level 0.00291, step 1, values float32
Opened empty_spike_230505_reconstruction.mrc as #15, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
Opened empty_spike_230505_reconstruction.mrc gaussian as #16, grid size
288,288,288, pixel 1.06, shown at level 0.00281, step 1, values float32
Opened DS1_NTR_C_long_spike_reconstruction.mrc as #13.1, grid size
300,300,300, pixel 1.06, shown at level 0.0051, step 2, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc as #13.2, grid size
300,300,300, pixel 1.06, shown at level 0.0177, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc as #13.3, grid size
300,300,300, pixel 1.06, shown at level 0.0189, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #17, grid size
300,300,300, pixel 1.06, shown at level 0.00438, step 1, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc gaussian as #18, grid size
300,300,300, pixel 1.06, shown at level 0.00246, step 1, values float32
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at level 0.00253, step 1, values float32
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at level 0.00354, step 1, values float32
Log from Thu Jul 25 23:02:46 2024UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:/Users/yulab/Desktop/DS1/DS1_TR.cxs
Opened long_full_spike_230505_reconstruction.mrc as #2, grid size 288,288,288,
pixel 1.06, shown at level 0.00465, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc as #4, grid size
288,288,288, pixel 1.06, shown at level 0.0226, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at level 0.00084, step 1, values float32
Opened long_full_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at level 0.00297, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at level 0.00291, step 1, values float32
Opened empty_spike_230505_reconstruction.mrc as #15, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
Opened empty_spike_230505_reconstruction.mrc gaussian as #16, grid size
288,288,288, pixel 1.06, shown at level 0.00281, step 1, values float32
Log from Thu Jul 18 13:20:09 2024UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/Rotavirus/【RV_DS-1】/【sub-particles for PPT 的图片】/2023.09.25/TR.cxs"
Opened long_full_2_spike_230505_reconstruction.mrc as #1, grid size
288,288,288, pixel 1.06, shown at level 0.00273, step 1, values float32
Opened long_full_spike_230505_reconstruction.mrc as #2, grid size 288,288,288,
pixel 1.06, shown at level 0.00465, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc as #4, grid size
288,288,288, pixel 1.06, shown at level 0.0226, step 1, values float32
Opened long_full_2_spike_230505_reconstruction.mrc gaussian as #5, grid size
288,288,288, pixel 1.06, shown at level 0.00084, step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at level 0.00084, step 1, values float32
Opened long_full_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at level 0.00297, step 1, values float32
Opened short_better_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at level 0.00291, step 1, values float32
Opened empty_spike_230505_reconstruction.mrc as #15, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
Opened empty_spike_230505_reconstruction.mrc gaussian as #16, grid size
288,288,288, pixel 1.06, shown at level 0.00281, step 1, values float32
Log from Sat Sep 23 15:58:12 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:/Users/lld/Desktop/DS1.cxs
Opened empty_spike_reconstruction.mrc gaussian as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0025, step 1, values float32
Opened short_2_spike_reconstruction.mrc gaussian as #4, grid size 288,288,288,
pixel 1.06, shown at level 0.00232, step 1, values float32
Opened short_better_spike_reconstruction.mrc gaussian as #2, grid size
288,288,288, pixel 1.06, shown at level 0.00251, step 1, values float32
Opened long_full_spike_reconstruction.mrc gaussian as #5, grid size
288,288,288, pixel 1.06, shown at level 0.00288, step 1, values float32
Opened long_full_2_spike_reconstruction.mrc as #1, grid size 288,288,288,
pixel 1.06, shown at level 0.0203, step 2, values float32
Opened long_full_2_spike_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at level 0.000384, step 1, values float32
Opened NTR_short_run_class001_job300.mrc gaussian as #8, grid size
256,256,256, pixel 1.06, shown at level 0.000206, step 1, values float32
Opened run_class001.mrc as #7, grid size 288,288,288, pixel 1.06, shown at
level 0.00442, step 1, values float32
Opened long_half_spike_reconstruction.mrc as #16, grid size 288,288,288, pixel
1.06, shown at level 0.0219, step 2, values float32
Opened long_half_spike_reconstruction.mrc gaussian as #17, grid size
288,288,288, pixel 1.06, shown at level 0.00136, step 1, values float32
Opened short_2_spike.mrc as #12, grid size 288,288,288, pixel 1.06, shown at
level 0.00412, step 1, values float32
Opened short_better_spike.mrc as #14, grid size 288,288,288, pixel 1.06, shown
at level 0.00556, step 1, values float32
Log from Mon Sep 11 18:46:51 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/lld/Desktop/RV_temp/empty_spike_reconstruction.mrc
Opened empty_spike_reconstruction.mrc as #1, grid size 288,288,288, pixel
1.06, shown at level 0.0195, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/short_2_spike_reconstruction.mrc
Opened short_2_spike_reconstruction.mrc as #2, grid size 288,288,288, pixel
1.06, shown at level 0.0194, step 2, values float32
> volume #1 step 1
> volume #1 level 0.00747
> volume #1 level 0.003379
> vop gaussian #1-2 sdev 1
Opened empty_spike_reconstruction.mrc gaussian as #3, grid size 288,288,288,
pixel 1.06, shown at step 1, values float32
Opened short_2_spike_reconstruction.mrc gaussian as #4, grid size 288,288,288,
pixel 1.06, shown at step 1, values float32
> hide #!4 models
> volume #3 level 0.01118
> volume #3 level 0.005004
> lighting soft
> volume #3 level 0.002503
> show #!4 models
> volume #4 level 0.00232
> close #1-2
> open C:/Users/lld/Desktop/RV_temp/short_better_spike_reconstruction.mrc
Opened short_better_spike_reconstruction.mrc as #1, grid size 288,288,288,
pixel 1.06, shown at level 0.0213, step 2, values float32
> vop gaussian #1 sdev 1
Opened short_better_spike_reconstruction.mrc gaussian as #2, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> hide #!4 models
> volume #2 level 0.002511
> show #!4 models
> hide #!2 models
> close #1
> open C:/Users/lld/Desktop/RV_temp/long_full_spike_reconstruction.mrc
Opened long_full_spike_reconstruction.mrc as #1, grid size 288,288,288, pixel
1.06, shown at level 0.0213, step 2, values float32
> hide #!4 models
> vop gaussian #1 sdev 1
Opened long_full_spike_reconstruction.mrc gaussian as #5, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> volume #5 level 0.001267
> volume #5 level 0.0023
> hide #!5 models
> show #!1 models
> volume #1 step 1
> volume #1 level 0.004292
> hide #!5 models
> close #1
> open C:/Users/lld/Desktop/RV_temp/long_full_2_spike_reconstruction.mrc
Opened long_full_2_spike_reconstruction.mrc as #1, grid size 288,288,288,
pixel 1.06, shown at level 0.0203, step 2, values float32
> vop gaussian #1 sdev 1
Opened long_full_2_spike_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> volume #6 level 0.0006134
> show #!5 models
> open
> D:/【Rotavirus_manuscript】_2023/Supplementary/2_NTR/short_spike/NTR_short_run_class001_job300.mrc
Opened NTR_short_run_class001_job300.mrc as #7, grid size 256,256,256, pixel
1.04, shown at level 0.00381, step 1, values float32
> hide #!6 models
> hide #!5 models
> volume #7 level 0.0002695
> volume #7 level 0.0009555
> volume #7 level 0.0007726
> show #!6 models
> hide #!7 models
> volume #6 level 0.003593
> show #!7 models
> select #7
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,6.7067,0,1,0,15.183,0,0,1,45.778
> view matrix models #7,1,0,0,3.1452,0,1,0,14.904,0,0,1,61.709
> hide #!6 models
> show #!6 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.14596,0.98904,0.022171,21.704,-0.98395,-0.14746,0.10053,288.52,0.1027,-0.0071418,0.99469,49.529
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.14596,0.98904,0.022171,8.5729,-0.98395,-0.14746,0.10053,316.24,0.1027,-0.0071418,0.99469,43.394
> ui tool show "Map Coordinates"
> view matrix models
> #7,-0.14596,0.98904,0.022171,14.373,-0.98395,-0.14746,0.10053,336.11,0.1027,-0.0071418,0.99469,41.227
> view matrix models
> #7,-0.14596,0.98904,0.022171,15.886,-0.98395,-0.14746,0.10053,335.51,0.1027,-0.0071418,0.99469,30.531
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.15123,0.98848,-0.0065679,-20.931,-0.98321,0.15111,0.10227,294.51,0.10208,-0.0090084,0.99474,30.863
> view matrix models
> #7,0.15153,0.98843,-0.0065983,-20.962,-0.98317,0.15141,0.10226,294.46,0.10208,-0.0090087,0.99474,30.864
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> view matrix models
> #7,0.88528,0.43469,-0.16528,-25.386,-0.41908,0.89976,0.1217,113.01,0.20161,-0.03847,0.97871,23.34
> show #!6 models
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.88528,0.43469,-0.16528,-34.047,-0.41908,0.89976,0.1217,63.854,0.20161,-0.03847,0.97871,24.565
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.89982,0.43534,-0.028393,-53.626,-0.43464,0.90018,0.027736,77.938,0.037634,-0.012617,0.99921,40.805
> ui tool show "Fit in Map"
Fit map NTR_short_run_class001_job300.mrc in map
long_full_2_spike_reconstruction.mrc gaussian using 854262 points
correlation = 0.9341, correlation about mean = 0.7117, overlap = 18.22
steps = 224, shift = 10.8, angle = 18 degrees
Position of NTR_short_run_class001_job300.mrc (#7) relative to
long_full_2_spike_reconstruction.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.98823862 0.14275993 -0.05480914 -14.19418066
-0.14524314 0.98840152 -0.04434941 26.38067106
0.04784212 0.05178845 0.99751145 35.72088354
Axis 0.29995439 -0.32027648 -0.89858241
Axis point 81.87079932 12.03192259 0.00000000
Rotation angle (degrees) 9.22164660
Shift along axis -44.80487276
> hide #!6 models
> show #!6 models
> ~select #7
Nothing selected
> vop gaussian #7 sdev 1
Opened NTR_short_run_class001_job300.mrc gaussian as #8, grid size
256,256,256, pixel 1.06, shown at step 1, values float32
> hide #!6 models
> lighting soft
> volume #8 level 0.0008567
> volume #8 color #55aa00
> volume #8 level 0.0001166
> show #!6 models
> volume #6 level 0.000728
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> volume #6 level 0.0003842
> show #!8 models
> volume #8 level 0.0002848
> volume #8 level 0.0002063
> hide #!8 models
> hide #!6 models
> show #!7 models
> close #7
> show #!5 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> open C:/Users/lld/AppData/Local/Temp/fz3-16944024240330
'C:/Users/lld/AppData/Local/Temp/fz3-16944024240330' has no suffix
> open C:/Users/lld/Desktop/RV_temp/run_class001.mrc
Opened run_class001.mrc as #7, grid size 288,288,288, pixel 1.06, shown at
level 0.0182, step 2, values float32
> hide #!5 models
> volume #7 step 1
> volume #7 level 0.005757
> volume #7 level 0.002104
> volume #7 level 0.003696
> close #7
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> open C:/Users/lld/Desktop/RV_temp/run_class001.mrc
Opened run_class001.mrc as #7, grid size 288,288,288, pixel 1.06, shown at
level 0.00431, step 2, values float32
> volume #7 step 1
> volume #7 level 0.008674
> volume #7 level 0.005512
> hide #!7 models
> open "D:/Rotavirus/【RV_DS-1】/4ds0__VP8 and A-type HBGA.pdb"
> "D:/Rotavirus/【RV_DS-1】/5vx5__VP8 of a G2P[4] HRVs in complex with
> LNFP1.pdb"
4ds0__VP8 and A-type HBGA.pdb title:
Cell attachment protein VP8* of A human rotavirus specifically interacts with
A-type histo-blood group antigen [more info...]
Chain information for 4ds0__VP8 and A-type HBGA.pdb #9
---
Chain | Description | UniProt
A | rotavirus cell attachment protein VP8* | Q86169_9REOV
Non-standard residues in 4ds0__VP8 and A-type HBGA.pdb #9
---
A2G — 2-acetamido-2-deoxy-α-D-galactopyranose
FUC — α-L-fucopyranose
GAL — β-D-galactopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
5vx5__VP8 of a G2P[4] HRVs in complex with LNFP1.pdb title:
VP8* of A G2P[4] human rotavirus In complex with LNFP1 [more info...]
Chain information for 5vx5__VP8 of a G2P[4] HRVs in complex with LNFP1.pdb #10
---
Chain | Description | UniProt
A | indian G2P[4] rotavirus VP8* | Q2VE61_9REOV
Non-standard residues in 5vx5__VP8 of a G2P[4] HRVs in complex with LNFP1.pdb
#10
---
BGC — β-D-glucopyranose
FUC — α-L-fucopyranose
GAL — β-D-galactopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> view
> hide #10 models
> hide #9 models
> show #10 models
> open
> D:/【Rotavirus_manuscript】_2023/Fig.1/VP4_long_spike_trypsin_free_230307.pdb
Chain information for VP4_long_spike_trypsin_free_230307.pdb #11
---
Chain | Description
C D | No description available
E | No description available
> hide #10 models
> mmaker #10 to #11
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 VP4_long_spike_trypsin_free_230307.pdb, chain C (#11) with
5vx5__VP8 of a G2P[4] HRVs in complex with LNFP1.pdb, chain A (#10), sequence
alignment score = 721.4
RMSD between 154 pruned atom pairs is 0.871 angstroms; (across all 161 pairs:
1.118)
> show #10 models
> mmaker #9 to #11
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 VP4_long_spike_trypsin_free_230307.pdb, chain C (#11) with
4ds0__VP8 and A-type HBGA.pdb, chain A (#9), sequence alignment score = 405
RMSD between 145 pruned atom pairs is 0.901 angstroms; (across all 162 pairs:
1.745)
> show #9 models
> hide #10 models
> hide #9 models
> show #10 models
> show #!7 models
> hide #10 models
> select #11
15816 atoms, 16134 bonds, 6 pseudobonds, 1983 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,0.54578,0,1,0,-6.7562,0,0,1,46.747
> ui tool show "Fit in Map"
Fit molecule VP4_long_spike_trypsin_free_230307.pdb (#11) to map
run_class001.mrc (#7) using 15816 atoms
average map value = 0.00609, steps = 148
shifted from previous position = 9.22
rotated from previous position = 10 degrees
atoms outside contour = 10362, contour level = 0.0055121
Position of VP4_long_spike_trypsin_free_230307.pdb (#11) relative to
run_class001.mrc (#7) coordinates:
Matrix rotation and translation
0.98867225 0.15008928 0.00061983 -19.50957503
-0.14943026 0.98470136 -0.08963167 35.29158068
-0.01406310 0.08852373 0.99597479 41.10955001
Axis 0.51075518 0.04209461 -0.85869505
Axis point 248.53140066 -0.23839827 0.00000000
Rotation angle (degrees) 10.04397093
Shift along axis -43.77959834
> volume #7 level 0.002793
> volume #7 level 0.004424
> mmaker #9 to #11
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 VP4_long_spike_trypsin_free_230307.pdb, chain C (#11) with
4ds0__VP8 and A-type HBGA.pdb, chain A (#9), sequence alignment score = 405
RMSD between 145 pruned atom pairs is 0.901 angstroms; (across all 162 pairs:
1.745)
> mmaker #10 to #11
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 VP4_long_spike_trypsin_free_230307.pdb, chain C (#11) with
5vx5__VP8 of a G2P[4] HRVs in complex with LNFP1.pdb, chain A (#10), sequence
alignment score = 721.4
RMSD between 154 pruned atom pairs is 0.871 angstroms; (across all 161 pairs:
1.118)
> show #10 models
> ~select #11
Nothing selected
> open C:/Users/lld/Desktop/RV_temp/mask.mrc
Opened mask.mrc as #12, grid size 288,288,288, pixel 1.06, shown at level
0.366, step 2, values float32
> volume #12 step 1
> volume #12 level 0.04846
> close #12
> open C:/Users/lld/Desktop/RV_temp/run_it039_class001.mrc
Opened run_it039_class001.mrc as #12, grid size 288,288,288, pixel 1.06, shown
at level 2.14e-06, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it039_class002.mrc
Opened run_it039_class002.mrc as #13, grid size 288,288,288, pixel 1.06, shown
at level 0.000192, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it039_class003.mrc
Opened run_it039_class003.mrc as #14, grid size 288,288,288, pixel 1.06, shown
at level 0.00149, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it039_class004.mrc
Opened run_it039_class004.mrc as #15, grid size 288,288,288, pixel 1.06, shown
at level 0.000961, step 2, values float32
> hide #10 models
> hide #!7 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> show #!12 models
> volume #12 step 1
> volume #12 level 0.00341
> volume #12 level 0.0003085
> volume #12 level 0.000117
> volume #14 step 1
> volume #14 level 0.0001493
> volume #15 level 0.0003498
> show #!5 models
> volume #15 step 1
> volume #15 level 0.00233
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!12 models
> hide #!15 models
[Repeated 1 time(s)]
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> open C:/Users/lld/Desktop/RV_temp/long_half_spike_reconstruction.mrc
Opened long_half_spike_reconstruction.mrc as #16, grid size 288,288,288, pixel
1.06, shown at level 0.0219, step 2, values float32
> vop gaussian #16 sdev 1
Opened long_half_spike_reconstruction.mrc gaussian as #17, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> hide #!6 models
> volume #17 level 0.001363
> ui mousemode right clip
> show #!5 models
> hide #!5 models
> show #!6 models
> close #12-15
> hide #!17 models
> hide #!6 models
> open C:/Users/lld/Desktop/RV_temp/run_it021_class001.mrc
Opened run_it021_class001.mrc as #12, grid size 288,288,288, pixel 1.06, shown
at level 4.08e-07, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it021_class002.mrc
Opened run_it021_class002.mrc as #13, grid size 288,288,288, pixel 1.06, shown
at level 8.49e-07, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it021_class003.mrc
Opened run_it021_class003.mrc as #14, grid size 288,288,288, pixel 1.06, shown
at level 1.28e-06, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it021_class004.mrc
Opened run_it021_class004.mrc as #15, grid size 288,288,288, pixel 1.06, shown
at level 2.86e-07, step 2, values float32
> volume #13 level 0.0002929
> volume #15 level 0.0002672
> close #12-15
> open C:/Users/lld/Desktop/RV_temp/run_it037_class001.mrc
Opened run_it037_class001.mrc as #12, grid size 288,288,288, pixel 1.06, shown
at level 1.04e-06, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it037_class002.mrc
Opened run_it037_class002.mrc as #13, grid size 288,288,288, pixel 1.06, shown
at level 7.74e-08, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it037_class003.mrc
Opened run_it037_class003.mrc as #14, grid size 288,288,288, pixel 1.06, shown
at level 8.86e-07, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/run_it037_class004.mrc
Opened run_it037_class004.mrc as #15, grid size 288,288,288, pixel 1.06, shown
at level 1.26e-07, step 2, values float32
> volume #13 level 0.0004615
> close #12-15
> show #!11 models
> show #10 models
> open C:/Users/lld/Desktop/RV_temp/mask.mrc
Opened mask.mrc as #12, grid size 288,288,288, pixel 1.06, shown at level 1,
step 2, values float32
> volume #12 level 0.689
> volume #12 level 0.8964
> hide #!12 models
> show #!5 models
> volume #5 level 0.0002156
> volume #5 level 0.004055
> volume #5 level 0.003616
> open "D:/Rotavirus/【RV_DS-1】/4ds0__VP8 and A-type HBGA.pdb"
4ds0__VP8 and A-type HBGA.pdb title:
Cell attachment protein VP8* of A human rotavirus specifically interacts with
A-type histo-blood group antigen [more info...]
Chain information for 4ds0__VP8 and A-type HBGA.pdb #13
---
Chain | Description | UniProt
A | rotavirus cell attachment protein VP8* | Q86169_9REOV
Non-standard residues in 4ds0__VP8 and A-type HBGA.pdb #13
---
A2G — 2-acetamido-2-deoxy-α-D-galactopyranose
FUC — α-L-fucopyranose
GAL — β-D-galactopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> hide #10 models
> mmaker #13 to #11
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 VP4_long_spike_trypsin_free_230307.pdb, chain C (#11) with
4ds0__VP8 and A-type HBGA.pdb, chain A (#13), sequence alignment score = 405
RMSD between 145 pruned atom pairs is 0.901 angstroms; (across all 162 pairs:
1.745)
> select #13
1630 atoms, 1392 bonds, 440 residues, 1 model selected
> hide sel target a
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.7829,-0.59258,0.18951,148.69,0.5173,-0.78926,-0.33087,165.62,0.34564,-0.161,0.92445,197.16
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.77323,0.60556,-0.18817,142.35,-0.63068,-0.76527,0.12885,177.77,-0.06597,0.21831,0.97365,199.59
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.77323,0.60556,-0.18817,138.76,-0.63068,-0.76527,0.12885,198.83,-0.06597,0.21831,0.97365,190.38
> view matrix models
> #13,-0.77323,0.60556,-0.18817,137.54,-0.63068,-0.76527,0.12885,193.12,-0.06597,0.21831,0.97365,176.36
> view matrix models
> #13,-0.77323,0.60556,-0.18817,141.79,-0.63068,-0.76527,0.12885,194.74,-0.06597,0.21831,0.97365,175.44
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.71634,0.65173,-0.2492,141.17,-0.68855,-0.71809,0.10123,195.45,-0.11297,0.24411,0.96315,176.01
> view matrix models
> #13,-0.30526,0.9519,0.026544,130.17,-0.94849,-0.30144,-0.097474,197.7,-0.084784,-0.054931,0.99488,177.73
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.30526,0.9519,0.026544,131.78,-0.94849,-0.30144,-0.097474,198.98,-0.084784,-0.054931,0.99488,177.68
> ui tool show "Fit in Map"
Fit molecule 4ds0__VP8 and A-type HBGA.pdb (#13) to map
long_full_spike_reconstruction.mrc gaussian (#5) using 1630 atoms
average map value = 0.0028, steps = 88
shifted from previous position = 1.77
rotated from previous position = 22.4 degrees
atoms outside contour = 928, contour level = 0.0036165
Position of 4ds0__VP8 and A-type HBGA.pdb (#13) relative to
long_full_spike_reconstruction.mrc gaussian (#5) coordinates:
Matrix rotation and translation
-0.40614427 0.87287727 -0.27042949 137.09575878
-0.91376352 -0.38498116 0.12971408 195.09737194
0.00911422 0.29979123 0.95396129 174.02565599
Axis 0.09363636 -0.15390342 -0.98363915
Axis point 130.88635817 33.58009379 0.00000000
Rotation angle (degrees) 114.74509957
Shift along axis -188.36745307
> ~select #13
Nothing selected
> select #13
1630 atoms, 1392 bonds, 440 residues, 1 model selected
> color sel forest green
> ui tool show "Color Zone"
> color zone #5 near sel distance 7
> color zone #5 near sel distance 5
> color zone #5 near sel distance 3
> select #11
15816 atoms, 16134 bonds, 6 pseudobonds, 1983 residues, 2 models selected
> color (#!11 & sel) cornflower blue
> hide #!5 models
Drag select of 2146 residues, 6 pseudobonds
> show #!5 models
> color zone #5 near sel distance 3
> select #5
2 models selected
> select clear
> ui mousemode right clip
> hide #!5 models
> select #13/A:224
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/A:223
12 atoms, 10 bonds, 2 residues, 1 model selected
> color sel red
> select #11/D:545
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/A:62
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #13/A:63
10 atoms, 8 bonds, 2 residues, 1 model selected
> color sel hot pink
Drag select of 2142 residues, 5 pseudobonds
> hide #!11 models
> hide #13 models
> show #!5 models
> color zone #5 near sel distance 3
> hide #!5 models
> show #!11 models
> show #13 models
> select clear
> select add #13/A:64
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #13/A:65
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #13/A:66
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #13/A:67
27 atoms, 23 bonds, 4 residues, 1 model selected
> color sel hot pink
Drag select of 1928 residues, 5 pseudobonds
> hide #!11 models
> hide #13 models
> show #!5 models
> color zone #5 near sel distance 3
> show #!11 models
> show #13 models
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #11/E:252
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #11/E:253
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #11/E:255
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #11/E:254
31 atoms, 27 bonds, 4 residues, 1 model selected
> select add #11/E:256
37 atoms, 32 bonds, 5 residues, 1 model selected
> color sel cyan
Drag select of 1928 residues, 5 pseudobonds
> color zone #5 near sel distance 3
> select clear
> show #!5 models
> lighting soft
> lighting simple
> ui tool show "Fit in Map"
Fit molecule VP4_long_spike_trypsin_free_230307.pdb (#11) to map
long_full_spike_reconstruction.mrc gaussian (#5) using 15816 atoms
average map value = 0.004754, steps = 160
shifted from previous position = 1.07
rotated from previous position = 3.69 degrees
atoms outside contour = 7736, contour level = 0.0036165
Position of VP4_long_spike_trypsin_free_230307.pdb (#11) relative to
long_full_spike_reconstruction.mrc gaussian (#5) coordinates:
Matrix rotation and translation
0.98883613 0.14207669 -0.04491461 -11.94725888
-0.14408321 0.98853621 -0.04512406 27.88631175
0.03798864 0.05109174 0.99797119 38.43516696
Axis 0.30732200 -0.26480052 -0.91402072
Axis point 109.23547663 -7.23116104 0.00000000
Rotation angle (degrees) 9.00606796
Shift along axis -46.18650420
> hide #!5 models
Drag select of 2120 residues, 5 pseudobonds
> color zone #5 near sel distance 3
> select clear
> show #!5 models
> show #!12 models
> hide #!12 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!11 models
> hide #13 models
> volume #5 level 0.001022
> volume #5 level 0.001854
> volume #5 level 0.004449
> show #13 models
> volume #5 level 0.002882
> lighting soft
> set bgColor white
> ui mousemode right clip
> lighting simple
> close #12
> hide #13 models
> hide #!5 models
> open C:/Users/lld/Desktop/RV_temp/1/short_2_spike.mrc
Opened short_2_spike.mrc as #12, grid size 288,288,288, pixel 1.06, shown at
level 0.0206, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/1/short_better_spike.mrc
Opened short_better_spike.mrc as #14, grid size 288,288,288, pixel 1.06, shown
at level 0.0237, step 2, values float32
> lighting soft
> set bgColor black
> volume #12 step 1
> volume #12 level 0.002657
> volume #12 level 0.004123
> volume #14 step 1
> volume #14 level 0.008052
> volume #14 level 0.005561
> hide #!14 models
> show #!5 models
> lighting simple
> save C:/Users/lld/Desktop/DS1.cxs includeMaps true
——— End of log from Mon Sep 11 18:46:51 2023 ———
opened ChimeraX session
> close #1-8,12,14,16-17
> open
> C:/Users/lld/Desktop/RV_temp/long_full_2_spike_230505_reconstruction.mrc
Opened long_full_2_spike_230505_reconstruction.mrc as #1, grid size
288,288,288, pixel 1.06, shown at level 0.021, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/long_full_spike_230505_reconstruction.mrc
Opened long_full_spike_230505_reconstruction.mrc as #2, grid size 288,288,288,
pixel 1.06, shown at level 0.0224, step 2, values float32
> open C:/Users/lld/Desktop/RV_temp/long_half_spike_230505_reconstruction.mrc
Opened long_half_spike_230505_reconstruction.mrc as #3, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
> open
> C:/Users/lld/Desktop/RV_temp/short_better_spike_230505_reconstruction.mrc
Opened short_better_spike_230505_reconstruction.mrc as #4, grid size
288,288,288, pixel 1.06, shown at level 0.0226, step 2, values float32
> lighting soft
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> volume #4 step 1
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> volume #2 level 0.008982
> volume #2 level 0.0057
> volume #2 level 0.00465
> show #!1 models
> volume #1 level 0.002725
> vop gaussian #1,3 sdev 1
Opened long_full_2_spike_230505_reconstruction.mrc gaussian as #5, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
Opened long_half_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> volume #5 level 0.0007146
> volume #6 level 0.000939
> vop gaussian #2 sdev 1
Opened long_full_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> volume #7 level 0.003771
> hide #!6 models
> hide #!7 models
> show #!4 models
> vop gaussian #4 sdev 1
Opened short_better_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> volume #8 level 0.003305
> hide #!8 models
> show #!7 models
> measure mapstats #5-8
Map long_full_2_spike_230505_reconstruction.mrc gaussian #5, minimum
-0.007982, maximum 0.0222, mean 6.964e-05, SD 0.002798, RMS 0.002799
Map long_half_spike_230505_reconstruction.mrc gaussian #6, minimum -0.009395,
maximum 0.02224, mean 6.577e-05, SD 0.002801, RMS 0.002801
Map long_full_spike_230505_reconstruction.mrc gaussian #7, minimum -0.009334,
maximum 0.02329, mean 6.021e-05, SD 0.002964, RMS 0.002965
Map short_better_spike_230505_reconstruction.mrc gaussian #8, minimum
-0.008516, maximum 0.02307, mean 5.695e-05, SD 0.002914, RMS 0.002914
> hide #!7 models
> show #!6 models
> ui mousemode right clip
> lighting simple
> hide #!6 models
> show #!7 models
> ui tool show "Side View"
> lighting soft
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> volume #5 level 0.001106
> volume #7 level 0.002986
> lighting simple
> volume #5 level 0.0007146
> lighting soft
> open D:/【Rotavirus_manuscript】_2023/Fig.2/upright_230307.pdb
Chain information for upright_230307.pdb #12
---
Chain | Description
C D | No description available
E | No description available
> ui tool show "Fit in Map"
Fit molecule upright_230307.pdb (#12) to map
long_full_spike_230505_reconstruction.mrc gaussian (#7) using 15725 atoms
average map value = 0.001606, steps = 108
shifted from previous position = 6.41
rotated from previous position = 3.44 degrees
atoms outside contour = 11285, contour level = 0.002986
Position of upright_230307.pdb (#12) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.99824475 -0.05810045 -0.01147875 6.63962223
0.05820649 0.99826281 0.00913002 -10.37430553
0.01092835 -0.00978213 0.99989243 -4.71158616
Axis -0.15767213 -0.18680987 0.96966054
Axis point 192.97430835 98.46850045 0.00000000
Rotation angle (degrees) 3.43826406
Shift along axis -3.67749996
> mmaker #12 to #11
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 VP4_long_spike_trypsin_free_230307.pdb, chain C (#11) with
upright_230307.pdb, chain C (#12), sequence alignment score = 3763.1
RMSD between 728 pruned atom pairs is 0.077 angstroms; (across all 729 pairs:
1.344)
Fit molecule upright_230307.pdb (#12) to map
long_full_spike_230505_reconstruction.mrc gaussian (#7) using 15725 atoms
average map value = 0.005434, steps = 76
shifted from previous position = 0.303
rotated from previous position = 0.189 degrees
atoms outside contour = 5686, contour level = 0.002986
Position of upright_230307.pdb (#12) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.98909147 0.14005493 -0.04563642 -11.73425685
-0.14202620 0.98891720 -0.04325884 27.54532048
0.03907203 0.04926852 0.99802104 38.66331738
Axis 0.29971512 -0.27438810 -0.91371878
Axis point 104.87142256 -7.34899769 0.00000000
Rotation angle (degrees) 8.87961269
Shift along axis -46.40244172
Fit molecule upright_230307.pdb (#12) to map
long_full_spike_230505_reconstruction.mrc gaussian (#7) using 15725 atoms
average map value = 0.005433, steps = 44
shifted from previous position = 0.0101
rotated from previous position = 0.0114 degrees
atoms outside contour = 5681, contour level = 0.002986
Position of upright_230307.pdb (#12) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.98909622 0.13999793 -0.04570835 -11.72235897
-0.14197977 0.98891604 -0.04343744 27.55388058
0.03912057 0.04945347 0.99800999 38.62886638
Axis 0.30084618 -0.27473582 -0.91324247
Axis point 104.93836645 -7.74948923 0.00000000
Rotation angle (degrees) 8.88099768
Shift along axis -46.37418617
> lighting simple
> lighting soft
> view name 1
> save C:/Users/lld/Desktop/RV_temp/TR.cxs includeMaps true
> hide #!7 models
Drag select of 750 residues, 2 pseudobonds
> select up
7682 atoms, 7854 bonds, 2 pseudobonds, 967 residues, 2 models selected
> select up
15725 atoms, 16043 bonds, 2 pseudobonds, 1972 residues, 2 models selected
> select up
15725 atoms, 16043 bonds, 6 pseudobonds, 1972 residues, 2 models selected
> select up
15725 atoms, 16043 bonds, 6 pseudobonds, 1972 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!12 & sel) red
> hide #!12 models
> show #!7 models
> color zone #7 near #12 distance 4
> select up
36560 atoms, 36359 bonds, 6 pseudobonds, 5400 residues, 22 models selected
> select down
15725 atoms, 16043 bonds, 6 pseudobonds, 1972 residues, 2 models selected
> select down
6 pseudobonds, 1 model selected
> select up
15725 atoms, 16043 bonds, 6 pseudobonds, 1972 residues, 2 models selected
> color zone #7 near #12 distance 5
> color zone #7 near #12 distance 4
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> set bgColor white
> measure mapstats #5-8
Map long_full_2_spike_230505_reconstruction.mrc gaussian #5, minimum
-0.007982, maximum 0.0222, mean 6.964e-05, SD 0.002798, RMS 0.002799
Map long_half_spike_230505_reconstruction.mrc gaussian #6, minimum -0.009395,
maximum 0.02224, mean 6.577e-05, SD 0.002801, RMS 0.002801
Map long_full_spike_230505_reconstruction.mrc gaussian #7, minimum -0.009334,
maximum 0.02329, mean 6.021e-05, SD 0.002964, RMS 0.002965
Map short_better_spike_230505_reconstruction.mrc gaussian #8, minimum
-0.008516, maximum 0.02307, mean 5.695e-05, SD 0.002914, RMS 0.002914
> hide #!7 models
> set bgColor black
> show #!5 models
> volume #5 level 0.0008397
> volume #6 level 0.0008403
> volume #7 level 0.0008895
> volume #7 level 0.002965
> view list
Named views: 1
> view 1
> volume #8 level 0.002914
> color #5 white models transparency 0
> show #!5 models
> set bgColor white
> hide #!8 models
> set bgColor black
> set bgColor white
> lighting simple
> lighting soft
> color #5 #d9d9d9 models transparency 0
> color #5 #e3e3e3 models transparency 0
> color #6 #e3e3e3 models transparency 0
> color #7 #e3e3e3 models transparency 0
> color #8 #e3e3e3 models transparency 0
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!12 models
> ui tool show "Color Actions"
> hide #!12 models
> show #!8 models
> hide #!8 models
> show #!7 models
> color sel pale green
Fit molecule upright_230307.pdb (#12) to map
long_full_spike_230505_reconstruction.mrc gaussian (#7) using 15725 atoms
average map value = 0.005434, steps = 496
shifted from previous position = 0.0188
rotated from previous position = 0.006 degrees
atoms outside contour = 5655, contour level = 0.002965
Position of upright_230307.pdb (#12) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.98909747 0.13996041 -0.04579612 -11.70217193
-0.14194497 0.98892286 -0.04339587 27.54843108
0.03921513 0.04942327 0.99800777 38.60300487
Axis 0.30065026 -0.27535975 -0.91311907
Axis point 104.76627917 -7.79999640 0.00000000
Rotation angle (degrees) 8.87991094
Shift along axis -46.35312986
> ui tool show "Color Zone"
> color zone #7 near sel distance 4
> save C:/Users/lld/Desktop/RV_temp/long_full.png width 1229 height 834
> supersample 3
> hide #!7 models
> show #!5 models
> show #!12 models
> color sel hot pink
Fit molecule upright_230307.pdb (#12) to map
long_full_2_spike_230505_reconstruction.mrc gaussian (#5) using 15725 atoms
average map value = 0.002702, steps = 620
shifted from previous position = 0.17
rotated from previous position = 0.141 degrees
atoms outside contour = 7174, contour level = 0.0008397
Position of upright_230307.pdb (#12) relative to
long_full_2_spike_230505_reconstruction.mrc gaussian (#5) coordinates:
Matrix rotation and translation
0.98921862 0.13914389 -0.04566728 -11.56528358
-0.14103248 0.98915080 -0.04111622 27.16652707
0.03945075 0.04711350 0.99811019 38.77219748
Axis 0.28849826 -0.27832352 -0.91613578
Axis point 101.42609649 -5.26639032 0.00000000
Rotation angle (degrees) 8.79572106
Shift along axis -46.41824508
> color zone #5 near sel distance 6.37
> hide #!12 models
> color zone #5 near sel distance 4
[Repeated 1 time(s)]
> save C:/Users/lld/Desktop/RV_temp/long_full_2.png width 1229 height 834
> supersample 3
> color sel salmon
> hide #!5 models
> show #!6 models
> color zone #6 near sel distance 4
> save C:/Users/lld/Desktop/RV_temp/long_half.png width 1229 height 834
> supersample 3
> view name 1
> hide #!6 models
> show #!8 models
> open D:/【Rotavirus_manuscript】/manuscript/model/wt_sub_VP5CT.pdb
Summary of feedback from opening
D:/【Rotavirus_manuscript】/manuscript/model/wt_sub_VP5CT.pdb
---
warnings | Ignored bad PDB record found on line 20
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 21
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 22
BOND : 0.008 0.090 37024
Ignored bad PDB record found on line 23
ANGLE : 0.870 18.360 50433
Ignored bad PDB record found on line 24
CHIRALITY : 0.053 0.416 5716
16 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (33 )
Cannot find LINK/SSBOND residue CYS (117 )
Cannot find LINK/SSBOND residue CYS (124 )
Cannot find LINK/SSBOND residue CYS (156 )
52 messages similar to the above omitted
Chain information for wt_sub_VP5CT.pdb #14
---
Chain | Description
T Z | No description available
e | No description available
> ~select #12
Nothing selected
> lighting simple
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,5.9242,0,1,0,-9.9806,0,0,1,48.022
> ui tool show "Fit in Map"
Fit molecule wt_sub_VP5CT.pdb (#14) to map
short_better_spike_230505_reconstruction.mrc gaussian (#8) using 6389 atoms
average map value = 0.007333, steps = 104
shifted from previous position = 11.6
rotated from previous position = 8.86 degrees
atoms outside contour = 969, contour level = 0.002914
Position of wt_sub_VP5CT.pdb (#14) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.98894803 0.13718810 -0.05622472 -10.67471702
-0.13943087 0.98949835 -0.03810575 26.88164629
0.05040661 0.04552407 0.99769070 38.58164221
Axis 0.27149929 -0.34617235 -0.89802719
Axis point 77.13044036 -8.69546105 0.00000000
Rotation angle (degrees) 8.85966286
Shift along axis -46.85122461
> lighting soft
> color sel dodger blue
> hide #!14 models
> color zone #8 near sel distance 4
> save C:/Users/lld/Desktop/RV_temp/short.png width 1229 height 834
> supersample 3
> open C:/Users/lld/Desktop/RV_temp/empty_spike_230505_reconstruction.mrc
Opened empty_spike_230505_reconstruction.mrc as #15, grid size 288,288,288,
pixel 1.06, shown at level 0.0209, step 2, values float32
> hide #!8 models
> vop gaussian #15 sdev 1
Opened empty_spike_230505_reconstruction.mrc gaussian as #16, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> measure mapstats #16
Map empty_spike_230505_reconstruction.mrc gaussian #16, minimum -0.007748,
maximum 0.02221, mean 6.656e-05, SD 0.002808, RMS 0.002809
> volume #16 level 0.002809
> view list
Named views: 1
> view 1
> color #16 #e3e3e3 models transparency 0
> save C:/Users/lld/Desktop/RV_temp/empty.png width 1229 height 834
> supersample 3
> hide #!16 models
> ~select #14
Nothing selected
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!5 models
> lighting simple
> lighting soft
> show #!7 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> save C:/Users/lld/Desktop/RV_temp/long_1.png width 1229 height 834
> supersample 3
> show #!7 models
> save C:/Users/lld/Desktop/RV_temp/long_2.png width 1229 height 834
> supersample 3
> view name 2
> hide #!7 models
> lighting simple
> hide #!6 models
> show #!6 models
> show #!7 models
> lighting soft
> view list
Named views: 1, 2
> view 1
> view 2
> save C:/Users/lld/Desktop/RV_temp/TR.cxs includeMaps true
——— End of log from Sat Sep 23 15:58:12 2023 ———
opened ChimeraX session
> view orient
[Repeated 1 time(s)]
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> close #1
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> close #5
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #9 models
> show #!2 models
> hide #9 models
> show #10 models
> hide #10 models
> close #9-10
> show #!11 models
> hide #!11 models
> close #11
> show #!12 models
> hide #!12 models
> show #13 models
> close #13
> show #!14 models
> show #!8 models
> hide #!14 models
> hide #!8 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!2 models
> hide #!16 models
> open D:/【Rotavirus_manuscript】_2023/Fig.1/sub_all_VP7+NAG.pdb
Chain information for sub_all_VP7+NAG.pdb #1
---
Chain | Description
D | No description available
E | No description available
F | No description available
H j | No description available
S | No description available
h | No description available
i | No description available
k | No description available
l m r | No description available
n | No description available
o | No description available
p | No description available
q | No description available
s | No description available
t | No description available
> show #!2 models
> hide #!2 models
> select #1
80535 atoms, 82338 bonds, 8 pseudobonds, 10046 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> select clear
> hide #!2 models
> hide #!1 models
> show #!1 models
> select ::name="BMA"::name="MAN"::name="NAG"
2135 atoms, 2275 bonds, 175 residues, 1 model selected
> show sel atoms
> select clear
> view list
Named views: 1, 2
> show #!7 models
> view 1
> view 2
> view 1
> hide #!1 models
> save C:/Users/lld/Desktop/RV_temp/LiYinxia_DS1/DS1_TR.cxs includeMaps true
——— End of log from Thu Jul 18 13:20:09 2024 ———
opened ChimeraX session
> hide #!7 models
> open C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 277 277 GLU P
2 LYS P 17 1 16
Start residue of secondary structure not found: HELIX 278 278 TYR P 24 ASN P
26 1 3
Start residue of secondary structure not found: HELIX 279 279 SER P 28 MET P
41 1 14
Start residue of secondary structure not found: HELIX 280 280 ALA P 75 MET P
100 1 26
Start residue of secondary structure not found: HELIX 281 281 GLU P 114 LEU P
119 1 6
3018 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
3470 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
1790 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
2127 messages similar to the above omitted
Chain information for all_VP2_DS1_sub.pdb #5
---
Chain | Description
1 | No description available
2 | No description available
Chain information for all_VP5+8_DS1_sub.pdb #9
---
Chain | Description
A B | No description available
C | No description available
Chain information for all_VP6_DS1_sub.pdb #10
---
Chain | Description
N O P T U V Z | No description available
Q R S | No description available
W X Y | No description available
Chain information for all_VP7_DS1_sub.pdb #11
---
Chain | Description
3 | No description available
A C G I | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> lighting simple
> hide #5,10#!9,11 atoms
> show #5,10#!9,11 cartoons
> hide #5 models
> hide #!9 models
> hide #10 models
> hide #!11 models
> open C:/Users/yulab/Desktop/DS1/DS1_NTR_C_long_spike_reconstruction.mrc
> C:/Users/yulab/Desktop/DS1/DS1_NTR_C_others_spike_reconstruction.mrc
> C:/Users/yulab/Desktop/DS1/DS1_NTR_C_short_spike_reconstruction.mrc
Opened DS1_NTR_C_long_spike_reconstruction.mrc as #13.1, grid size
300,300,300, pixel 1.06, shown at level 0.0193, step 2, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc as #13.2, grid size
300,300,300, pixel 1.06, shown at level 0.0177, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc as #13.3, grid size
300,300,300, pixel 1.06, shown at level 0.0189, step 2, values float32
> hide #!13 models
> hide #!13.1 models
> hide #!13.2 models
> hide #!13.3 models
> show #!13.3 models
> show #!1 models
> hide #!1 models
> hide #!13.3 models
> show #!11 models
> color #11 magenta transparency 0
> color #11 #ff007f transparency 0
> color #11 cyan transparency 0
> color #11 #ffff7f transparency 0
> color #11 #aaaaff transparency 0
> color #11 #ffaa00 transparency 0
> color #11 #ff007f transparency 0
Drag select of 36 residues
> select up
822 atoms, 840 bonds, 116 residues, 1 model selected
> select up
6564 atoms, 6712 bonds, 896 residues, 1 model selected
> color sel cyan
> select #11
134588 atoms, 137391 bonds, 13 pseudobonds, 17165 residues, 2 models selected
> select clear
> hide #!11 models
> show #10 models
> color #10 #aaaaff transparency 0
> color #9 #ffaa00 transparency 0
> show #!9 models
> hide #10 models
> select #9
46989 atoms, 47943 bonds, 18 pseudobonds, 5892 residues, 2 models selected
> hide #!13 models
> ~select #9
Nothing selected
> hide #!9 models
> show #!9 models
> show #!9 cartoons
> show #10 models
> hide #!9 models
> hide #10 models
> show #!9 models
> show #10 models
> ui tool show "Side View"
[Repeated 1 time(s)]
> show #!11 models
> hide #!11 models
> hide #10 models
> hide #!9 models
> color #14 #ffaa00 transparency 0
> show #!14 models
> hide #!14 models
> show #!13.3 models
> save "C:/Users/yulab/Desktop/session 1-2024.7.cxs"
> color #13.3 #ff007f models transparency 0
> volume gaussian #13.3 sDev 3
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #17, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #17
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #17, minimum -0.002965,
maximum 0.008636, mean 6.088e-05, SD 0.001877, RMS 0.001878
> measure mapstats #17
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #17, minimum -0.002965,
maximum 0.008636, mean 6.088e-05, SD 0.001877, RMS 0.001878
> volume #17 level 0.001878
> volume gausssian #17 sd 1
Expected a density maps specifier or a keyword
> close #17
> show #!13.3 models
> volume gausssian #13.3 sd 1
Expected a density maps specifier or a keyword
> volume gaussian #13.3 sDev 1
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #17, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> volume gaussian #13.3 sDev 2
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #18, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!17 models
> hide #!18 models
> show #!17 models
> close #18
> measure mapstats #17
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #17, minimum -0.008048,
maximum 0.02086, mean 6.261e-05, SD 0.002563, RMS 0.002564
> volume #17 level 0.002564
> lighting simple
> show #!8 models
> ui mousemode right "rotate selected models"
> select #8
2 models selected
> view matrix models
> #8,0.85007,-0.52665,-0.0039021,103.47,0.52645,0.84949,0.03483,-61.325,-0.015028,-0.031662,0.99939,7.1808
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.85007,-0.52665,-0.0039021,119.83,0.52645,0.84949,0.03483,-85.407,-0.015028,-0.031662,0.99939,8.4681
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.83969,-0.543,0.0087036,122.42,0.5407,0.8374,0.080076,-91.043,-0.05077,-0.062533,0.99675,18.919
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.83969,-0.543,0.0087036,130.82,0.5407,0.8374,0.080076,-91.737,-0.05077,-0.062533,0.99675,9.887
> view matrix models
> #8,0.83969,-0.543,0.0087036,124.1,0.5407,0.8374,0.080076,-92.528,-0.05077,-0.062533,0.99675,9.5969
> view matrix models
> #8,0.83969,-0.543,0.0087036,128.63,0.5407,0.8374,0.080076,-95.91,-0.05077,-0.062533,0.99675,5.8634
> view matrix models
> #8,0.83969,-0.543,0.0087036,125.09,0.5407,0.8374,0.080076,-99.246,-0.05077,-0.062533,0.99675,7.0681
> view matrix models
> #8,0.83969,-0.543,0.0087036,-0.71254,0.5407,0.8374,0.080076,43.976,-0.05077,-0.062533,0.99675,2.2524
> view matrix models
> #8,0.83969,-0.543,0.0087036,123.93,0.5407,0.8374,0.080076,-93.261,-0.05077,-0.062533,0.99675,-1.359
> view matrix models
> #8,0.83969,-0.543,0.0087036,122.37,0.5407,0.8374,0.080076,-96.703,-0.05077,-0.062533,0.99675,1.2521
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.83812,-0.54549,0.0026628,123.69,0.54449,0.83687,0.0564,-94.423,-0.032994,-0.04582,0.9984,-4.1929
> view matrix models
> #8,0.83127,-0.55562,0.0168,124.62,0.55541,0.83143,0.015925,-90.508,-0.022816,-0.0039074,0.99973,-12.28
> view matrix models
> #8,0.87093,-0.48769,-0.060317,117.29,0.48879,0.87239,0.0041501,-85.221,0.050596,-0.033097,0.99817,-18.829
> view matrix models
> #8,0.86767,-0.49707,-0.0082722,113.1,0.49709,0.8677,0.00068758,-85.364,0.006836,-0.0047086,0.99997,-16.7
> view matrix models
> #8,0.85325,-0.52127,-0.015466,119.83,0.51946,0.85216,-0.063069,-78.925,0.046055,0.045779,0.99789,-30.114
> view matrix models
> #8,0.86763,-0.49585,-0.036748,116.27,0.49208,0.86692,-0.079474,-75.077,0.071265,0.050871,0.99616,-34.525
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.86763,-0.49585,-0.036748,113.03,0.49208,0.86692,-0.079474,-47.33,0.071265,0.050871,0.99616,-19.154
> view matrix models
> #8,0.86763,-0.49585,-0.036748,123.17,0.49208,0.86692,-0.079474,-57.415,0.071265,0.050871,0.99616,-20.525
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.86926,-0.49202,0.048026,112.39,0.4939,0.86019,-0.127,-51.093,0.021177,0.13412,0.99074,-24.938
> view matrix models
> #8,0.86786,-0.49665,0.012926,117.43,0.4944,0.8608,-0.12079,-51.991,0.048862,0.11122,0.99259,-25.884
> view matrix models
> #8,0.87145,-0.4903,0.013269,115.87,0.48791,0.86381,-0.12562,-50.893,0.05013,0.11595,0.99199,-26.726
> view matrix models
> #8,0.9349,-0.34901,0.064504,78.691,0.3543,0.90695,-0.22786,-25.124,0.021026,0.23588,0.97155,-38.158
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.9349,-0.34901,0.064504,68.402,0.3543,0.90695,-0.22786,-16.814,0.021026,0.23588,0.97155,-34.413
> view matrix models
> #8,0.9349,-0.34901,0.064504,72.103,0.3543,0.90695,-0.22786,-17.56,0.021026,0.23588,0.97155,-41.58
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.96991,-0.24133,-0.032263,61.73,0.22482,0.93856,-0.26183,1.3241,0.093468,0.2467,0.96458,-53.437
> view matrix models
> #8,0.97704,-0.20845,-0.044061,57.022,0.20322,0.9739,-0.10109,-19.624,0.063982,0.089813,0.9939,-28.502
> view matrix models
> #8,0.98218,-0.18136,-0.049387,52.74,0.18286,0.98275,0.027749,-32.986,0.043502,-0.036285,0.99839,-6.7122
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.362,0.18286,0.98275,0.027749,-58.99,0.043502,-0.036285,0.99839,-9.3012
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.665,0.18286,0.98275,0.027749,-55.487,0.043502,-0.036285,0.99839,-13.061
> ui tool show "Fit in Map"
> hide #!13 models
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2327732 points
correlation = 0.6132, correlation about mean = 0.2136, overlap = 61.74
steps = 220, shift = 13.5, angle = 11.2 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.94330562 0.33153171 -0.01616230 -47.80050159
-0.32988872 0.94179122 0.06482846 74.55968761
0.03671421 -0.05582129 0.99776553 14.23745777
Axis -0.17889666 -0.07840406 -0.98073890
Axis point 191.06140785 182.92840156 0.00000000
Rotation angle (degrees) 19.70668838
Shift along axis -11.25766096
> view matrix models
> #8,0.98218,-0.18136,-0.049387,54.677,0.18286,0.98275,0.027749,-56.191,0.043502,-0.036285,0.99839,-12.666
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.367,0.18286,0.98275,0.027749,-56.608,0.043502,-0.036285,0.99839,-12.698
> view matrix models
> #8,0.98218,-0.18136,-0.049387,55.896,0.18286,0.98275,0.027749,-56.588,0.043502,-0.036285,0.99839,-13.708
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2327732 points
correlation = 0.6132, correlation about mean = 0.2136, overlap = 61.74
steps = 68, shift = 1.3, angle = 0.00258 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.94330613 0.33152937 -0.01618109 -47.79907229
-0.32988683 0.94179469 0.06478759 74.55684696
0.03671826 -0.05577661 0.99776788 14.23380962
Axis -0.17877449 -0.07843998 -0.98075830
Axis point 191.05437090 182.92257418 0.00000000
Rotation angle (degrees) 19.70615091
Shift along axis -11.26291025
> hide #!8 models
> ~select #8
Nothing selected
> show #!14 models
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.98895,0.13719,-0.056225,4.3598,-0.13943,0.9895,-0.038106,2.5312,0.050407,0.045524,0.99769,35.983
> view matrix models
> #14,0.98895,0.13719,-0.056225,7.1942,-0.13943,0.9895,-0.038106,2.1067,0.050407,0.045524,0.99769,27.257
> view matrix models
> #14,0.98895,0.13719,-0.056225,0.90233,-0.13943,0.9895,-0.038106,-3.4835,0.050407,0.045524,0.99769,26.325
> view matrix models
> #14,0.98895,0.13719,-0.056225,2.0432,-0.13943,0.9895,-0.038106,-3.0306,0.050407,0.045524,0.99769,24.323
Fit molecule wt_sub_VP5CT.pdb (#14) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 6389 atoms
average map value = 0.007936, steps = 76
shifted from previous position = 1.83
rotated from previous position = 11.6 degrees
atoms outside contour = 587, contour level = 0.002564
Position of wt_sub_VP5CT.pdb (#14) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.97876004 -0.20487052 -0.00754054 55.22328801
0.20257034 0.97211837 -0.11811493 -34.29111638
0.03152856 0.11407868 0.99297130 18.54345442
Axis 0.49341696 -0.08302277 0.86582153
Axis point 169.74558733 140.80366832 -0.00000000
Rotation angle (degrees) 13.60880516
Shift along axis 46.15037265
> hide #!14 models
> ~select #14
Nothing selected
> color #17 #ff007f models transparency 0
> show #10 models
Fit molecule all_VP6_DS1_sub.pdb (#10) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 177623 atoms
average map value = 0.002805, steps = 344
shifted from previous position = 39
rotated from previous position = 11.3 degrees
atoms outside contour = 117770, contour level = 0.002564
Position of all_VP6_DS1_sub.pdb (#10) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.94131758 -0.33558694 0.03609191 70.11596237
0.33712883 0.93999065 -0.05255224 -54.29794975
-0.01629022 0.06163597 0.99796575 -19.49512610
Axis 0.16685745 0.07654335 0.98300545
Axis point 190.70484863 181.36558709 0.00000000
Rotation angle (degrees) 20.00931802
Shift along axis -11.62059144
> hide #10 models
> color #5 #ffff7f transparency 0
> show #5 models
Fit molecule all_VP2_DS1_sub.pdb (#5) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 51920 atoms
average map value = 0.002309, steps = 180
shifted from previous position = 18.2
rotated from previous position = 7.56 degrees
atoms outside contour = 37490, contour level = 0.002564
Position of all_VP2_DS1_sub.pdb (#5) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.98051129 -0.08864679 0.17532643 -8.16051665
0.09094379 0.99584300 -0.00509407 -14.83919525
-0.17414602 0.02093964 0.98449718 38.34149758
Axis 0.06611256 0.88748479 0.45607003
Axis point 203.98739165 0.00000000 70.64364046
Rotation angle (degrees) 11.35511001
Shift along axis 3.77733514
> color zone #17 near #5,10,14 distance 5
> color zone #17 near #5,10,14 distance 6
[Repeated 1 time(s)]
> hide #5 models
> lighting soft
> lighting simple
> lighting soft
> show #5 models
> select #5
51920 atoms, 52864 bonds, 6348 residues, 1 model selected
> view matrix models
> #5,0.99305,0.068034,0.096081,-9.4057,-0.073597,0.99574,0.055592,-1.3423,-0.091889,-0.062277,0.99382,55.662
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99623,-0.027574,0.082275,4.4522,0.028409,0.99956,-0.0089991,-17.592,-0.08199,0.011302,0.99657,43.099
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99623,-0.027574,0.082275,5.5747,0.028409,0.99956,-0.0089991,-24.732,-0.08199,0.011302,0.99657,11.742
> view matrix models
> #5,0.99623,-0.027574,0.082275,6.5493,0.028409,0.99956,-0.0089991,-26.232,-0.08199,0.011302,0.99657,6.7631
Fit molecule all_VP2_DS1_sub.pdb (#5) to map
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) using 51920 atoms
average map value = 0.00224, steps = 452
shifted from previous position = 26.7
rotated from previous position = 14.4 degrees
atoms outside contour = 36400, contour level = 0.002564
Position of all_VP2_DS1_sub.pdb (#5) relative to
DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) coordinates:
Matrix rotation and translation
0.95964191 -0.27667745 0.05036866 44.50660950
0.26800351 0.95400895 0.13431696 -46.14744395
-0.08521462 -0.11539720 0.98965749 51.76643797
Axis -0.40647351 0.22069639 0.88660723
Axis point 213.40575678 155.61982973 0.00000000
Rotation angle (degrees) 17.88885458
Shift along axis 17.62116619
> view matrix models
> #5,0.99356,-0.11319,-0.0053704,19.168,0.11175,0.97083,0.21214,-39.663,-0.018799,-0.21138,0.97722,34.887
> color zone #17 near #5,10,14 distance 6
> view matrix models
> #5,0.99356,-0.11319,-0.0053704,16.987,0.11175,0.97083,0.21214,-40,-0.018799,-0.21138,0.97722,28.544
> color zone #17 near #5,10,14 distance 6
> ~select #5
Nothing selected
> hide #5 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> save "C:/Users/yulab/Desktop/2024.7.23图/DS1-NTR-C-short spike(1)
> -2024.7.22.png" width 1133 height 834 supersample 3 transparentBackground
> true
> save "C:/Users/yulab/Desktop/session 2-2024.7.22.cxs"
> hide #!17 models
> show #!13.2 models
> volume gaussian #13.2 sDev 1
Opened DS1_NTR_C_others_spike_reconstruction.mrc gaussian as #18, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> color #18 #ff007f models transparency 0
> measure mapstats #18
Map DS1_NTR_C_others_spike_reconstruction.mrc gaussian #18, minimum -0.007177,
maximum 0.02053, mean 6.839e-05, SD 0.002456, RMS 0.002456
> volume #18 level 0.002456
> lighting simple
> hide #!13 models
> show #10 models
> select #10
177623 atoms, 181534 bonds, 22241 residues, 1 model selected
> ~select #10
Nothing selected
> hide #10 models
> show #!16 models
> select #16
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #16,1,0,0,-106.26,0,1,0,113.61,0,0,1,-13.881
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.92526,-0.37537,0.054773,238.87,0.37723,-0.89527,0.23703,322.48,-0.039938,0.23998,0.96996,-41.518
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.92526,-0.37537,0.054773,332.39,0.37723,-0.89527,0.23703,199.22,-0.039938,0.23998,0.96996,-26.371
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.92401,-0.36072,0.12684,323.2,0.38089,-0.89744,0.22254,200.35,0.033553,0.25394,0.96664,-39.375
> view matrix models
> #16,-0.72826,-0.66881,0.14948,338.18,0.68515,-0.70583,0.17994,128.85,-0.014843,0.23346,0.97225,-29.415
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.72826,-0.66881,0.14948,352.42,0.68515,-0.70583,0.17994,140.57,-0.014843,0.23346,0.97225,-31.434
> view matrix models
> #16,-0.72826,-0.66881,0.14948,361.13,0.68515,-0.70583,0.17994,147.26,-0.014843,0.23346,0.97225,-60.152
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.70345,-0.69292,0.15818,360.21,0.71068,-0.6827,0.16989,140.79,-0.0097281,0.23192,0.97269,-60.737
> view matrix models
> #16,-0.71411,-0.68093,0.16243,359.61,0.69341,-0.71989,0.030628,162.16,0.096075,0.1345,0.98625,-63.286
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.71411,-0.68093,0.16243,357.72,0.69341,-0.71989,0.030628,155.99,0.096075,0.1345,0.98625,-50.025
> view matrix models
> #16,-0.71411,-0.68093,0.16243,358,0.69341,-0.71989,0.030628,156.93,0.096075,0.1345,0.98625,-33.859
Fit map DS1_NTR_C_others_spike_reconstruction.mrc gaussian in map
empty_spike_230505_reconstruction.mrc gaussian using 2302533 points
correlation = 0.9823, correlation about mean = 0.9249, overlap = 120.9
steps = 176, shift = 14.3, angle = 9.37 degrees
Position of DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) relative
to empty_spike_230505_reconstruction.mrc gaussian (#16) coordinates:
Matrix rotation and translation
-0.76287057 0.64655077 0.00078575 171.53501680
-0.64643597 -0.76275694 0.01795592 380.69180111
0.01220875 0.01319010 0.99983848 7.71372779
Axis -0.00368573 -0.00883418 -0.99995419
Axis point 155.54487590 158.86396943 0.00000000
Rotation angle (degrees) 139.72004016
Shift along axis -11.70870508
> view matrix models
> #16,-0.71411,-0.68093,0.16243,325.64,0.69341,-0.71989,0.030628,-50.403,0.096075,0.1345,0.98625,-39.098
> view matrix models
> #16,-0.71411,-0.68093,0.16243,322.94,0.69341,-0.71989,0.030628,-110.64,0.096075,0.1345,0.98625,-40.972
> ~select #16
Nothing selected
> hide #!16 models
> show #10 models
> select #10
177623 atoms, 181534 bonds, 22241 residues, 1 model selected
> view matrix models
> #10,0.98111,-0.18701,-0.049511,52.398,0.18866,0.98155,0.031035,-56.187,0.042793,-0.03979,0.99829,-18.82
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.97166,-0.21632,0.095297,47.157,0.21495,0.97632,0.02452,-59.044,-0.098344,-0.003341,0.99515,-1.803
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.97166,-0.21632,0.095297,37.329,0.21495,0.97632,0.02452,-51.258,-0.098344,-0.003341,0.99515,-1.4087
> view matrix models
> #10,0.97166,-0.21632,0.095297,42.312,0.21495,0.97632,0.02452,-41.798,-0.098344,-0.003341,0.99515,20.301
Fit molecule all_VP6_DS1_sub.pdb (#10) to map
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) using 177623 atoms
average map value = 0.002757, steps = 204
shifted from previous position = 15.1
rotated from previous position = 7.08 degrees
atoms outside contour = 116820, contour level = 0.002456
Position of all_VP6_DS1_sub.pdb (#10) relative to
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) coordinates:
Matrix rotation and translation
0.94137430 -0.33545721 0.03581746 70.11996810
0.33698068 0.94004963 -0.05244719 -54.28364204
-0.01607640 0.06144223 0.99798116 -19.52134176
Axis 0.16650848 0.07586979 0.98311683
Axis point 190.75248955 181.46648830 0.00000000
Rotation angle (degrees) 19.99833713
Shift along axis -11.63467861
> ~select #10
Nothing selected
> show #5 models
> select #5
51920 atoms, 52864 bonds, 6348 residues, 1 model selected
> view matrix models
> #5,0.99356,-0.11319,-0.0053704,9.4846,0.11175,0.97083,0.21214,-14.909,-0.018799,-0.21138,0.97722,50.039
Fit molecule all_VP2_DS1_sub.pdb (#5) to map
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) using 51920 atoms
average map value = 0.002139, steps = 184
shifted from previous position = 23.6
rotated from previous position = 4.86 degrees
atoms outside contour = 36596, contour level = 0.002456
Position of all_VP2_DS1_sub.pdb (#5) relative to
DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#18) coordinates:
Matrix rotation and translation
0.97084006 -0.15935805 -0.17909378 30.26220993
0.20278518 0.94435644 0.25897700 -36.03533098
0.12785830 -0.28774281 0.94913452 41.17398645
Axis -0.75507027 -0.42392901 0.50015306
Axis point 0.00000000 95.98689081 138.45626346
Rotation angle (degrees) 21.22506545
Shift along axis 13.01962273
> view matrix models
> #5,0.98941,-0.14384,-0.01926,7.1637,0.14328,0.94714,0.28706,-13.496,-0.023048,-0.28678,0.95772,50.019
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.69234,-0.61336,0.38008,342.53,0.49025,-0.78634,-0.37594,195.7,0.52945,-0.073943,0.84511,-69.07
> view matrix models
> #5,0.83761,-0.4122,-0.35846,74.991,0.34132,0.90726,-0.24573,-33.733,0.42651,0.083475,0.90062,-76.561
> view matrix models
> #5,0.656,-0.69054,0.30464,138.57,0.75441,0.58766,-0.29243,-51.947,0.022909,0.42166,0.90646,-62.207
> view matrix models
> #5,0.61624,-0.78149,0.097629,160.65,0.78246,0.59345,-0.1886,-58.396,0.089454,0.19262,0.97719,-39.546
> view matrix models
> #5,0.47087,-0.86462,0.17527,195.51,0.87564,0.43387,-0.21215,-49.352,0.10739,0.25337,0.96139,-51.294
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.47087,-0.86462,0.17527,193.17,0.87564,0.43387,-0.21215,-52.757,0.10739,0.25337,0.96139,-55.651
> color zone #18 near #5,10 distance 5
> color zone #18 near #5,10 distance 3
> color zone #18 near #5,10 distance 5
> color zone #18 near #5,10 distance 6
> hide #10 models
> select clear
> hide #5 models
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> save "C:/Users/yulab/Desktop/session 3-2024.7.22.cxs"
> save "C:/Users/yulab/Desktop/中期图-2024.7.22/DS1-NTR-C-other
> spike(1)-2024.7.22.png" width 1133 height 833 supersample 3
> transparentBackground true
> lighting simple
[Repeated 2 time(s)]
> show #10 models
> hide #10 models
> show #!7 models
> select #7
3 models selected
> lighting simple
> ~select #7
Nothing selected
> hide #!7 models
> show #!16 models
> hide #!16 models
> hide #!18 models
> show #!13.2 models
> hide #!13.2 models
> hide #!13 models
> show #!18 models
> show #!13.2 models
> hide #!13.2 models
> show #!8 models
> hide #!8 models
> show #!16 models
> hide #!18 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> hide #!13 models
> show #10 models
> show #!11 models
> open C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
> C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP2_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 277 277 GLU P
2 LYS P 17 1 16
Start residue of secondary structure not found: HELIX 278 278 TYR P 24 ASN P
26 1 3
Start residue of secondary structure not found: HELIX 279 279 SER P 28 MET P
41 1 14
Start residue of secondary structure not found: HELIX 280 280 ALA P 75 MET P
100 1 26
Start residue of secondary structure not found: HELIX 281 281 GLU P 114 LEU P
119 1 6
3018 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP5+8_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
3470 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP6_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
1790 messages similar to the above omitted
Summary of feedback from opening
C:/Users/yulab/Desktop/DS1/all_VP7_DS1_sub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS 1 109
GLU 1 117 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP 1 167 LEU 1 182
1 16
Start residue of secondary structure not found: HELIX 3 3 LEU 1 191 MET 1 194
1 4
Start residue of secondary structure not found: HELIX 4 4 SER 1 210 GLN 1 221
1 12
Start residue of secondary structure not found: HELIX 5 5 GLY 1 227 ALA 1 234
1 8
2127 messages similar to the above omitted
Chain information for all_VP2_DS1_sub.pdb #19
---
Chain | Description
1 | No description available
2 | No description available
Chain information for all_VP5+8_DS1_sub.pdb #20
---
Chain | Description
A B | No description available
C | No description available
Chain information for all_VP6_DS1_sub.pdb #21
---
Chain | Description
N O P T U V Z | No description available
Q R S | No description available
W X Y | No description available
Chain information for all_VP7_DS1_sub.pdb #22
---
Chain | Description
3 | No description available
A C G I | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
> hide #10,19,21#!11,20,22 atoms
> show #10,19,21#!11,20,22 cartoons
> hide #10 models
> hide #!11 models
> show #!6 models
> show #!7 models
> hide #!6 models
> lighting soft
> hide #19 models
> hide #!20 models
> hide #21 models
> hide #!22 models
> show #!13.1 models
> hide #!7 models
> hide #!13.1 models
> show #!2 models
> hide #!2 models
> show #!17 models
> show #!8 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select #17
2 models selected
> lighting simple
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.56195,0.76777,0.30781,99.788,-0.6625,-0.64057,0.38829,314.58,0.49529,0.014274,0.86861,-68.948
> view matrix models
> #17,-0.67121,0.73935,0.053328,150.16,-0.73471,-0.67309,0.084584,365.25,0.098432,0.017593,0.99499,-20.69
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.67121,0.73935,0.053328,159.29,-0.73471,-0.67309,0.084584,349.66,0.098432,0.017593,0.99499,-20.541
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2327732 points
correlation = 0.9804, correlation about mean = 0.9225, overlap = 131
steps = 128, shift = 4.73, angle = 7.06 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#17) relative
to short_better_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
-0.76295156 0.64645517 0.00079553 171.56089352
-0.64633921 -0.76283691 0.01804085 380.69185933
0.01226947 0.01325011 0.99983694 7.69192724
Axis -0.00370555 -0.00887489 -0.99995375
Axis point 155.54416810 158.86533475 0.00000000
Rotation angle (degrees) 139.72724187
Shift along axis -11.70589662
> lighting soft
> ~select #17
Nothing selected
> volume #17 level 0.00438
> hide #!17 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> close #10#9,11
> hide #!7 models
> hide #!13 models
> save "C:/Users/yulab/Desktop/session 4-2024.7.25.cxs"
> show #!17 models
> hide #!17 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> volume gaussian #13.1 sDev 3
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!9 models
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.00343,
maximum 0.008499, mean 6.071e-05, SD 0.001891, RMS 0.001892
> volume #10 level 0.001892
> lighting simple
> close #10
> show #!9 models
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #9 level 0.002589
> volume gaussian #9 sDev 3
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.003382,
maximum 0.00813, mean 6.036e-05, SD 0.001871, RMS 0.001872
> volume #10 level 0.001872
> close #10
> show #!9 models
> show #!18 models
> hide #!18 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> show #!8 models
> measure mapstats #8
Map short_better_spike_230505_reconstruction.mrc gaussian #8, minimum
-0.008516, maximum 0.02307, mean 5.695e-05, SD 0.002914, RMS 0.002914
> hide #!8 models
> show #!7 models
> measure mapstats #7
Map long_full_spike_230505_reconstruction.mrc gaussian #7, minimum -0.009334,
maximum 0.02329, mean 6.021e-05, SD 0.002964, RMS 0.002965
> hide #!7 models
> close #9
> show #!13.1 models
> measure mapstats #13.1
Map DS1_NTR_C_long_spike_reconstruction.mrc #13.1, step 2, minimum -0.03056,
maximum 0.05107, mean 6.433e-05, SD 0.005103, RMS 0.005103
> volume #13.1 level 0.005103
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #9 level 0.002243
> show #!2 models
> hide #!2 models
> show #!7 models
> lighting simple
> hide #!7 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!9 models
> hide #!9 models
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!13 models
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #9 level 0.002589
> hide #!9 models
> show #!7 models
> hide #!7 models
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> hide #!13 models
> volume #9 level 0.002243
> color #9 #ff007f models transparency 0
> volume #9 level 0.002101
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!2 models
> measure mapstats #2
Map long_full_spike_230505_reconstruction.mrc #2, minimum -0.01726, maximum
0.05362, mean 5.97e-05, SD 0.004433, RMS 0.004434
> volume gaussian #2 sDev 1.5
Opened long_full_spike_230505_reconstruction.mrc gaussian as #10, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> measure mapstats #10
Map long_full_spike_230505_reconstruction.mrc gaussian #10, minimum -0.005654,
maximum 0.01589, mean 6.052e-05, SD 0.002548, RMS 0.002549
> volume #10 level 0.002549
> hide #!10 models
> show #!7 models
> show #!10 models
> select #10
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,20.985,0,1,0,54.766,0,0,1,5.9414
> volume #10 level 0.002319
> volume #10 level 0.002434
> volume #10 level 0.002578
> volume #10 level 0.002722
> volume #10 level 0.002981
> hide #!7 models
> close #10
> show #!9 models
> hide #!9 models
> close #9
> show #!13.3 models
> hide #!13.3 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #9 level 0.002243
> volume #9 level 0.002527
> volume #9 level 0.002583
> volume #9 level 0.002754
> volume #9 level 0.00264
> volume #9 level 0.002243
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1.3
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.006865,
maximum 0.01703, mean 6.177e-05, SD 0.002347, RMS 0.002348
> volume #9 level 0.002348
> close #9
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #9 level 0.002589
> volume #9 level 0.003085
> close #9
> hide #!7 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> measure mapstats #9
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #9, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #9 level 0.002243
> volume #9 level 0.002271
> volume #9 level 0.002356
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!9 models
> volume #9 level 0.00243
> lighting soft
> lighting simple
> hide #!9 models
> show #!2 models
> hide #!2 models
> show #!7 models
> lighting soft
> hide #!7 models
> hide #!13 models
> show #!9 models
> volume #9 level 0.002629
> lighting simple
> volume #9 level 0.002827
> volume #9 level 0.002884
> volume #9 level 0.002856
> volume #9 level 0.002941
> volume #9 level 0.003054
> volume #9 level 0.002912
> hide #!9 models
> show #!13.1 models
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> volume gaussian #13.1 sDev 1
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #11, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> close #11
> show #!10 models
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.009071,
maximum 0.02186, mean 6.198e-05, SD 0.002588, RMS 0.002589
> volume #10 level 0.002589
> volume #10 level 0.003375
> volume #10 level 0.00292
> volume #10 level 0.003003
> hide #!10 models
> show #!9 models
> volume #10 level 0.003044
> hide #!10 models
> volume #9 level 0.004416
> volume #9 level 0.002243
> volume #10 level 0.00354
> volume #10 level 0.003954
> volume #10 level 0.00354
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!9 models
> hide #!13 models
> hide #!10 models
> show #!9 models
> volume #9 level 0.002442
> color #9 #ff007f models transparency 0
> color #19 #ffff7f transparency 0
> color #20 #ffaa00 transparency 0
> color #21 #aaaaff transparency 0
> color #22 #ff007f transparency 0
> hide #!9 models
> show #!22 models
Drag select of 38 residues
Drag select of 43 residues
> select up
708 atoms, 724 bonds, 99 residues, 1 model selected
> select up
6564 atoms, 6712 bonds, 896 residues, 1 model selected
> color sel cyan
> hide #!22 models
> select #22
134588 atoms, 137391 bonds, 13 pseudobonds, 17165 residues, 2 models selected
> ~select #22
Nothing selected
> show #!9 models
> volume #9 level 0.002669
> volume #9 level 0.002442
> show #!7 models
> lighting simple
> lighting soft
> lighting simple
> volume #9 level 0.001732
> volume #9 level 0.001874
> volume #9 level 0.00213
> volume #9 level 0.002215
> volume #9 level 0.002385
> volume #9 level 0.002527
> select #9
2 models selected
> lighting simple
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,43.72,0,1,0,63.396,0,0,1,13.798
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.89844,-0.062288,0.43466,296.7,-0.002853,-0.98904,-0.14763,400.42,0.43909,-0.13388,0.88841,-19.615
> view matrix models
> #9,-0.91234,-0.0034031,0.40942,292.9,-0.037352,-0.9951,-0.091506,399.35,0.40772,-0.098777,0.90775,-22.817
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.91234,-0.0034031,0.40942,288.58,-0.037352,-0.9951,-0.091506,399.35,0.40772,-0.098777,0.90775,-32.331
> view matrix models
> #9,-0.91234,-0.0034031,0.40942,309.99,-0.037352,-0.9951,-0.091506,401.51,0.40772,-0.098777,0.90775,6.1498
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.87986,-0.19825,0.43191,332.86,0.15091,-0.97835,-0.14166,375.68,0.45064,-0.059458,0.89072,-4.6446
> view matrix models
> #9,-0.96122,-0.21995,0.16634,384.76,0.16318,-0.93991,-0.2999,388.79,0.22231,-0.26113,0.93936,57.199
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.96122,-0.21995,0.16634,307.45,0.16318,-0.93991,-0.2999,349.68,0.22231,-0.26113,0.93936,43.488
> view matrix models
> #9,-0.96122,-0.21995,0.16634,380.96,0.16318,-0.93991,-0.2999,403.55,0.22231,-0.26113,0.93936,34.507
> view matrix models
> #9,-0.96122,-0.21995,0.16634,381.96,0.16318,-0.93991,-0.2999,409.85,0.22231,-0.26113,0.93936,32.445
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.95244,-0.30471,0.0021292,416.04,0.29354,-0.91937,-0.26191,380.81,0.081765,-0.24883,0.96509,49.342
> view matrix models
> #9,-0.95924,-0.27698,0.055967,405.5,0.27577,-0.9608,-0.028455,358.99,0.061655,-0.011861,0.99803,10.381
> view matrix models
> #9,-0.5567,0.8305,-0.018998,175.26,-0.82503,-0.55541,-0.10415,479.21,-0.097052,-0.042308,0.99438,40.9
> view matrix models
> #9,-0.56056,0.82548,0.066024,165.29,-0.82558,-0.55084,-0.12242,481.01,-0.064688,-0.12313,0.99028,49.188
> view matrix models
> #9,-0.56118,0.82263,0.09145,162.44,-0.82587,-0.54918,-0.12779,481.51,-0.054898,-0.14724,0.98758,51.836
> view matrix models
> #9,-0.59534,0.80011,0.073425,173.86,-0.80188,-0.58592,-0.11702,482.11,-0.050607,-0.12854,0.99041,47.798
> view matrix models
> #9,-0.58505,0.80568,0.092679,168.77,-0.81099,-0.58168,-0.062843,475.63,0.0032781,-0.11193,0.99371,36.16
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.58505,0.80568,0.092679,130.22,-0.81099,-0.58168,-0.062843,374.32,0.0032781,-0.11193,0.99371,19.778
> view matrix models
> #9,-0.58505,0.80568,0.092679,125,-0.81099,-0.58168,-0.062843,380.1,0.0032781,-0.11193,0.99371,5.2713
> view matrix models
> #9,-0.58505,0.80568,0.092679,104.66,-0.81099,-0.58168,-0.062843,374.27,0.0032781,-0.11193,0.99371,15.125
> view matrix models
> #9,-0.58505,0.80568,0.092679,97.694,-0.81099,-0.58168,-0.062843,399.91,0.0032781,-0.11193,0.99371,26.632
> view matrix models
> #9,-0.58505,0.80568,0.092679,90.44,-0.81099,-0.58168,-0.062843,371.78,0.0032781,-0.11193,0.99371,27.287
> view matrix models
> #9,-0.58505,0.80568,0.092679,89.593,-0.81099,-0.58168,-0.062843,399.57,0.0032781,-0.11193,0.99371,36.592
> view matrix models
> #9,-0.58505,0.80568,0.092679,98.072,-0.81099,-0.58168,-0.062843,398.35,0.0032781,-0.11193,0.99371,37.952
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2710167 points
correlation = 0.9517, correlation about mean = 0.8579, overlap = 109.2
steps = 244, shift = 19.3, angle = 15.6 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#9) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76287030 0.64655109 0.00077330 171.53152575
-0.64643797 -0.76275816 0.01783070 380.69357438
0.01211830 0.01310262 0.99984072 7.71169534
Axis -0.00365654 -0.00877385 -0.99995482
Axis point 155.54381176 158.86562713 0.00000000
Rotation angle (degrees) 139.71998356
Shift along axis -11.67870565
> ~select #9
Nothing selected
> hide #!7 models
> show #19 models
> show #!20 models
> show #21 models
> show #!22 models
> hide #!22 models
> color zone #9 near #19-21 distance 3
> hide #19 models
> hide #!20 models
> hide #21 models
> undo
> hide #21 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!7 models
> select #9
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76287,0.64655,0.0007733,148.04,-0.64644,-0.76276,0.017831,280.61,0.012118,0.013103,0.99984,-1.7344
> view matrix models
> #9,-0.76287,0.64655,0.0007733,163.34,-0.64644,-0.76276,0.017831,378.69,0.012118,0.013103,0.99984,9.9129
> view matrix models
> #9,-0.76287,0.64655,0.0007733,168.77,-0.64644,-0.76276,0.017831,380.66,0.012118,0.013103,0.99984,13.013
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2710167 points
correlation = 0.9517, correlation about mean = 0.8578, overlap = 109.2
steps = 72, shift = 5.98, angle = 0.00666 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#9) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76294544 0.64646242 0.00077488 171.56141207
-0.64634927 -0.76283327 0.01783355 380.69276441
0.01211982 0.01310518 0.99984067 7.70607456
Axis -0.00365726 -0.00877501 -0.99995481
Axis point 155.54607252 158.86541448 0.00000000
Rotation angle (degrees) 139.72664358
Shift along axis -11.67375328
> hide #!7 models
> color zone #9 near #19-21 distance 2
> color zone #9 near #19-21 distance 4
> color zone #9 near #19-21 distance 5
> show #!7 models
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76295,0.64646,0.00077488,139.81,-0.64635,-0.76283,0.017834,325.48,0.01212,0.013105,0.99984,2.5638
> view matrix models
> #9,-0.76295,0.64646,0.00077488,138.24,-0.64635,-0.76283,0.017834,306.38,0.01212,0.013105,0.99984,6.6514
> view matrix models
> #9,-0.76295,0.64646,0.00077488,115.61,-0.64635,-0.76283,0.017834,252.16,0.01212,0.013105,0.99984,9.4588
> view matrix models
> #9,-0.76295,0.64646,0.00077488,183.03,-0.64635,-0.76283,0.017834,367.52,0.01212,0.013105,0.99984,1.5735
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.14,-0.64635,-0.76283,0.017834,381.01,0.01212,0.013105,0.99984,1.1846
> view matrix models
> #9,-0.76295,0.64646,0.00077488,173.78,-0.64635,-0.76283,0.017834,378,0.01212,0.013105,0.99984,3.21
> view matrix models
> #9,-0.76295,0.64646,0.00077488,171.33,-0.64635,-0.76283,0.017834,377.7,0.01212,0.013105,0.99984,3.3809
> view matrix models
> #9,-0.76295,0.64646,0.00077488,173.06,-0.64635,-0.76283,0.017834,377.86,0.01212,0.013105,0.99984,7.232
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.61,-0.64635,-0.76283,0.017834,377.88,0.01212,0.013105,0.99984,7.4313
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.43,-0.64635,-0.76283,0.017834,379.38,0.01212,0.013105,0.99984,7.0262
> view matrix models
> #9,-0.76295,0.64646,0.00077488,169.28,-0.64635,-0.76283,0.017834,371.66,0.01212,0.013105,0.99984,3.4371
> hide #!7 models
> ui tool show "Side View"
> color zone #9 near #19-21 distance 5
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> select #9
3 models selected
> hide #!9 models
> show #!9 models
> color zone #9 near #19-21 distance 5
> ~select #9
Nothing selected
> color zone #9 near #19-21 distance 5
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!7 models
> select #9
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76295,0.64646,0.00077488,171.99,-0.64635,-0.76283,0.017834,379.07,0.01212,0.013105,0.99984,9.1529
> lighting simple
> view matrix models
> #9,-0.76295,0.64646,0.00077488,142.27,-0.64635,-0.76283,0.017834,351.15,0.01212,0.013105,0.99984,9.6988
> view matrix models
> #9,-0.76295,0.64646,0.00077488,172.57,-0.64635,-0.76283,0.017834,379.46,0.01212,0.013105,0.99984,6.5396
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2710167 points
correlation = 0.9518, correlation about mean = 0.8583, overlap = 109.2
steps = 56, shift = 1.99, angle = 0.00204 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#9) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76296775 0.64643609 0.00077787 171.56500444
-0.64632300 -0.76285572 0.01782507 380.69833753
0.01211617 0.01309720 0.99984082 7.73400902
Axis -0.00365703 -0.00877023 -0.99995485
Axis point 155.54508055 158.86913542 0.00000000
Rotation angle (degrees) 139.72862075
Shift along axis -11.69988868
> hide #!7 models
> color zone #9 near #19-21 distance 3
> lighting soft
> lighting simple
> color zone #9 near #19-21 distance 5
> lighting soft
> lighting simple
> lighting soft
> ~select #9
Nothing selected
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> save "C:/Users/yulab/Desktop/session 5-2024.7.25.cxs" includeMaps true
——— End of log from Thu Jul 25 23:02:46 2024 ———
opened ChimeraX session
> hide #!9 models
> show #21 models
> show #!22 models
> lighting simple
> show #!20 models
> ui tool show "Side View"
> hide #!20 models
> show #19 models
> hide #19 models
> show #!9 models
> hide #!9 models
> show #!14 models
> hide #!14 models
> show #5 models
> hide #5 models
> show #5 models
> close #5
> show #19 models
> show #!20 models
> hide #19 models
> hide #!20 models
> hide #21 models
> hide #!22 models
> close #6-8
> show #!9 models
> hide #!9 models
> show #!10 models
> close #10
> show #!17 models
> close #17
> close #18
> open C:/Users/yulab/Desktop/DS1/DS1_NTR_C_long_spike_reconstruction.mrc
> C:/Users/yulab/Desktop/DS1/DS1_NTR_C_others_spike_reconstruction.mrc
> C:/Users/yulab/Desktop/DS1/DS1_NTR_C_short_spike_reconstruction.mrc
Opened DS1_NTR_C_long_spike_reconstruction.mrc as #5.1, grid size 300,300,300,
pixel 1.06, shown at level 0.0193, step 2, values float32
Opened DS1_NTR_C_others_spike_reconstruction.mrc as #5.2, grid size
300,300,300, pixel 1.06, shown at level 0.0177, step 2, values float32
Opened DS1_NTR_C_short_spike_reconstruction.mrc as #5.3, grid size
300,300,300, pixel 1.06, shown at level 0.0189, step 2, values float32
> hide #!5 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> show #!16 models
> close #16
> show #!22 models
> hide #!22 models
> show #!2 models
> volume gaussian #2 sDev 1.5
Opened long_full_spike_230505_reconstruction.mrc gaussian as #6, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> color #6 #ff007f models transparency 0
> color #6 #ffff7f models transparency 0
> color #6 yellow models transparency 0
> color #6 #ffaa00 models transparency 0
> color #6 #aaaaff models transparency 0
> color #6 cyan models transparency 0
> color #6 #ff007f models transparency 0
> measure mapstats #6
Map long_full_spike_230505_reconstruction.mrc gaussian #6, minimum -0.005654,
maximum 0.01589, mean 6.052e-05, SD 0.002548, RMS 0.002549
> volume #6 level 0.002549
> show #!20 models
> show #19 models
> show #21 models
> show #!22 models
> hide #!6 models
> show #!6 models
> color zone #6 near #19-22 distance 3
> color zone #6 near #19-22 distance 5
> hide #19 models
> hide #!20 models
> hide #21 models
> hide #!22 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> hide #!6 models
> show #!4 models
> volume gaussian #4 sDev 1.5
Opened short_better_spike_230505_reconstruction.mrc gaussian as #7, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> color #7 #ff007f models transparency 0
> measure mapstats #7
Map short_better_spike_230505_reconstruction.mrc gaussian #7, minimum
-0.005468, maximum 0.01566, mean 5.71e-05, SD 0.002483, RMS 0.002484
> volume #7 level 0.002484
> show #!4 models
> hide #!7 models
> show #!7 models
> hide #!4 models
> hide #!7 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!6 models
> show #!7 models
> show #!14 models
> select #14
6389 atoms, 6536 bonds, 3 pseudobonds, 799 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.99309,-0.057292,-0.10241,28.434,0.054758,0.99812,-0.027386,-8.1151,0.10379,0.021589,0.99436,24.588
> view matrix models
> #14,0.99309,-0.057292,-0.10241,33.497,0.054758,0.99812,-0.027386,-5.7846,0.10379,0.021589,0.99436,28.304
> view matrix models
> #14,0.99309,-0.057292,-0.10241,34.885,0.054758,0.99812,-0.027386,2.0806,0.10379,0.021589,0.99436,26.501
> view matrix models
> #14,0.99309,-0.057292,-0.10241,30.486,0.054758,0.99812,-0.027386,0.60982,0.10379,0.021589,0.99436,25.891
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.98286,0.14085,-0.11897,-0.39556,-0.14606,0.98861,-0.036198,31.373,0.11251,0.052954,0.99224,19.499
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.98286,0.14085,-0.11897,0.30634,-0.14606,0.98861,-0.036198,26.72,0.11251,0.052954,0.99224,20.554
> ui tool show "Fit in Map"
Fit molecule wt_sub_VP5CT.pdb (#14) to map
short_better_spike_230505_reconstruction.mrc gaussian (#7) using 6389 atoms
average map value = 0.004978, steps = 96
shifted from previous position = 9.06
rotated from previous position = 3.64 degrees
atoms outside contour = 1166, contour level = 0.002484
Position of wt_sub_VP5CT.pdb (#14) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.98907341 0.13641694 -0.05589460 -10.60577892
-0.13866292 0.98959185 -0.03847808 26.80890226
0.05006378 0.04580815 0.99769496 38.60818939
Axis 0.27491097 -0.34559760 -0.89721026
Axis point 77.42660097 -10.40672957 0.00000000
Rotation angle (degrees) 8.81805985
Shift along axis -46.82040106
> show #19 models
> show #!20 models
> show #!22 models
> show #21 models
> hide #!20 models
> hide #!7 models
> ~select #14
Nothing selected
> hide #!14 models
> show #!20 models
> hide #!20 models
> show #!14 models
> show #!7 models
> color zone #7 near #14,19,21,22 distance 5
> hide #19 models
> hide #21 models
> hide #!22 models
> hide #!14 models
> lighting simple
> lighting soft
> lighting simple
> hide #!7 models
> show #!15 models
> volume gaussian #15 sDev 1.5
Opened empty_spike_230505_reconstruction.mrc gaussian as #8, grid size
288,288,288, pixel 1.06, shown at step 1, values float32
> color #8 #ff007f models transparency 0
> measure mapstats #8
Map empty_spike_230505_reconstruction.mrc gaussian #8, minimum -0.006069,
maximum 0.01536, mean 6.648e-05, SD 0.002436, RMS 0.002437
> volume #8 level 0.002437
> show #21 models
> show #!22 models
> show #19 models
> color zone #8 near #19,21,22 distance 5
> hide #19 models
> hide #21 models
> hide #!22 models
> lighting soft
> hide #!8 models
> show #!5.1 models
> volume gaussian #5.1 sDev 1.5
Opened DS1_NTR_C_long_spike_reconstruction.mrc gaussian as #10, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!5 models
> measure mapstats #10
Map DS1_NTR_C_long_spike_reconstruction.mrc gaussian #10, minimum -0.005914,
maximum 0.01531, mean 6.163e-05, SD 0.002242, RMS 0.002243
> volume #10 level 0.002243
> lighting simple
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> close #9
> show #!10 models
> color #10 #ff007f models transparency 0
> color #10 springgreen models transparency 0
> show #!6 models
> lighting simple
> select #10
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.059108,-0.99785,0.028313,304.25,0.95514,0.048288,-0.29218,39.8,0.29019,0.044314,0.95594,-47.086
> view matrix models
> #10,0.0043409,-0.98839,0.15189,294.61,0.981,-0.025251,-0.19236,33.814,0.19396,0.14983,0.9695,-50.467
> view matrix models
> #10,-0.07261,-0.99736,0.00011256,328.91,0.99522,-0.072461,-0.065524,21.805,0.065359,-0.0046456,0.99785,-9.335
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.07261,-0.99736,0.00011256,295.48,0.99522,-0.072461,-0.065524,-148.66,0.065359,-0.0046456,0.99785,-14.234
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.051168,-0.99828,-0.028687,296.14,0.97995,-0.044649,-0.19416,-133.15,0.19255,-0.038047,0.98055,-26.735
> view matrix models
> #10,-0.30034,0.88373,0.35892,-16.742,-0.94356,-0.22019,-0.2474,207.16,-0.1396,-0.41297,0.89998,96.61
> view matrix models
> #10,-0.68749,0.72452,-0.0493,125.6,-0.72154,-0.68918,-0.066435,221.96,-0.08211,-0.010101,0.99657,10.2
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.68749,0.72452,-0.0493,172.93,-0.72154,-0.68918,-0.066435,391.26,-0.08211,-0.010101,0.99657,14.765
> view matrix models
> #10,-0.68749,0.72452,-0.0493,172.88,-0.72154,-0.68918,-0.066435,390.78,-0.08211,-0.010101,0.99657,15.874
> view matrix models
> #10,-0.68749,0.72452,-0.0493,155.2,-0.72154,-0.68918,-0.066435,393.22,-0.08211,-0.010101,0.99657,29.386
> view matrix models
> #10,-0.68749,0.72452,-0.0493,155.77,-0.72154,-0.68918,-0.066435,394.94,-0.08211,-0.010101,0.99657,28.675
> view matrix models
> #10,-0.68749,0.72452,-0.0493,158.49,-0.72154,-0.68918,-0.066435,398.7,-0.08211,-0.010101,0.99657,30.498
> view matrix models
> #10,-0.68749,0.72452,-0.0493,158.38,-0.72154,-0.68918,-0.066435,399.68,-0.08211,-0.010101,0.99657,29.106
> view matrix models
> #10,-0.68749,0.72452,-0.0493,154.23,-0.72154,-0.68918,-0.066435,400.13,-0.08211,-0.010101,0.99657,27.211
> view matrix models
> #10,-0.68749,0.72452,-0.0493,154.33,-0.72154,-0.68918,-0.066435,399.47,-0.08211,-0.010101,0.99657,27.577
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2902464 points
correlation = 0.984, correlation about mean = 0.9133, overlap = 95.81
steps = 152, shift = 11.2, angle = 8.29 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#10) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#6) coordinates:
Matrix rotation and translation
-0.76287363 0.64654717 0.00076320 171.53657951
-0.64643609 -0.76276343 0.01767265 380.69837368
0.01200834 0.01298863 0.99984353 7.73420650
Axis -0.00362248 -0.00869666 -0.99995562
Axis point 155.54695565 158.86746136 0.00000000
Rotation angle (degrees) 139.72024012
Shift along axis -11.66605716
> save "C:/Users/yulab/Desktop/session 6-2024.7.26.cxs"
Fit map DS1_NTR_C_long_spike_reconstruction.mrc gaussian in map
long_full_spike_230505_reconstruction.mrc gaussian using 2902464 points
correlation = 0.984, correlation about mean = 0.9133, overlap = 95.81
steps = 44, shift = 0.00367, angle = 0.00196 degrees
Position of DS1_NTR_C_long_spike_reconstruction.mrc gaussian (#10) relative to
long_full_spike_230505_reconstruction.mrc gaussian (#6) coordinates:
Matrix rotation and translation
-0.76285506 0.64656907 0.00076728 171.53062720
-0.64645815 -0.76274515 0.01765444 380.70107044
0.01200006 0.01297176 0.99984385 7.74171881
Axis -0.00362132 -0.00868681 -0.99995571
Axis point 155.54757659 158.86851153 0.00000000
Rotation angle (degrees) 139.71859344
Shift along axis -11.66962052
> ~select #10
Nothing selected
> hide #!10 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!10 models
> color #10 #ff007f models transparency 0
> show #19 models
> show #!20 models
> show #21 models
> color zone #10 near #19-21 distance 5
> hide #19 models
> hide #!20 models
> hide #21 models
> lighting soft
> lighting simple
> hide #!10 models
> show #!5.3 models
> volume guassian #5.3 sd 1.5
Expected a density maps specifier or a keyword
> volume gaussian #5.3 sDev 1.5
Opened DS1_NTR_C_short_spike_reconstruction.mrc gaussian as #9, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!5 models
> measure mapstats #9
Map DS1_NTR_C_short_spike_reconstruction.mrc gaussian #9, minimum -0.004597,
maximum 0.0151, mean 6.214e-05, SD 0.00223, RMS 0.002231
> volume #9 level 0.002231
> show #!7 models
> select #9
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-163.86,0,1,0,46.93,0,0,1,9.2155
> view matrix models #9,1,0,0,-250.67,0,1,0,77.257,0,0,1,20.309
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.99936,-0.0099564,-0.034277,-245.14,0.015054,0.98829,0.15182,59.725,0.032365,-0.15224,0.98781,40.77
> view matrix models
> #9,-0.9383,0.24642,-0.24263,44.749,-0.28773,-0.9455,0.15245,415.44,-0.19184,0.21285,0.95807,21.562
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.9383,0.24642,-0.24263,277.83,-0.28773,-0.9455,0.15245,338.12,-0.19184,0.21285,0.95807,67.859
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.96584,0.19016,-0.17607,283.69,-0.2295,-0.94319,0.24026,318.68,-0.12038,0.27246,0.95461,47.425
> view matrix models
> #9,-0.95674,0.18605,-0.22367,288.24,-0.22052,-0.96523,0.14038,331.95,-0.18977,0.18363,0.9645,71.461
> view matrix models
> #9,-0.96397,0.2451,-0.10334,266.51,-0.25349,-0.96421,0.07769,344.04,-0.080604,0.10109,0.99161,64.244
> view matrix models
> #9,-0.96447,0.24432,-0.10049,266.39,-0.25306,-0.96363,0.085927,342.96,-0.07584,0.1083,0.99122,62.384
> view matrix models
> #9,-0.78187,0.61156,-0.12111,181.29,-0.62222,-0.7776,0.090422,371.41,-0.038876,0.14606,0.98851,50.816
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.78187,0.61156,-0.12111,199.38,-0.62222,-0.7776,0.090422,361.92,-0.038876,0.14606,0.98851,-8.375
> view matrix models
> #9,-0.78187,0.61156,-0.12111,200.85,-0.62222,-0.7776,0.090422,364.7,-0.038876,0.14606,0.98851,-8.2374
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.84218,0.52641,-0.1167,223.47,-0.53654,-0.83963,0.084591,361.63,-0.053455,0.13385,0.98956,-4.1003
> view matrix models
> #9,-0.84743,0.52724,-0.062212,218.07,-0.53045,-0.83602,0.14037,353.84,0.021996,0.15195,0.98814,-18.79
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.84743,0.52724,-0.062212,213.38,-0.53045,-0.83602,0.14037,347.36,0.021996,0.15195,0.98814,-18.168
> view matrix models
> #9,-0.84743,0.52724,-0.062212,215.27,-0.53045,-0.83602,0.14037,347.14,0.021996,0.15195,0.98814,-17.789
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.79007,0.60981,-0.062689,193.09,-0.61143,-0.77652,0.15222,349.19,0.044146,0.15859,0.98636,-22.16
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2828369 points
correlation = 0.9834, correlation about mean = 0.9161, overlap = 94.12
steps = 160, shift = 17.1, angle = 8.88 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#9) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76288802 0.64653014 0.00079618 171.54954391
-0.64641668 -0.76277610 0.01783497 380.69121271
0.01213815 0.01309142 0.99984062 7.69778686
Axis -0.00366862 -0.00877179 -0.99995480
Axis point 155.54940712 158.86257327 0.00000000
Rotation angle (degrees) 139.72156843
Shift along axis -11.66613402
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.76289,0.64653,0.00079618,172.43,-0.64642,-0.76278,0.017835,375.74,0.012138,0.013091,0.99984,-0.70094
> view matrix models
> #9,-0.76289,0.64653,0.00079618,171.48,-0.64642,-0.76278,0.017835,372.96,0.012138,0.013091,0.99984,-7.6391
> view matrix models
> #9,-0.76289,0.64653,0.00079618,172.72,-0.64642,-0.76278,0.017835,372.8,0.012138,0.013091,0.99984,-7.5864
> view matrix models
> #9,-0.76289,0.64653,0.00079618,172.61,-0.64642,-0.76278,0.017835,375.99,0.012138,0.013091,0.99984,-7.6989
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2828369 points
correlation = 0.9835, correlation about mean = 0.9163, overlap = 94.12
steps = 112, shift = 16.1, angle = 0.000267 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#9) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76289022 0.64652754 0.00079928 171.54142616
-0.64641405 -0.76277835 0.01783428 380.68815313
0.01214003 0.01308893 0.99984063 7.70593439
Axis -0.00367003 -0.00877088 -0.99995480
Axis point 155.54438536 158.86267521 0.00000000
Rotation angle (degrees) 139.72176504
Shift along axis -11.67411769
> hide #!7 models
> show #!7 models
> hide #!7 models
> ~select #9
Nothing selected
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #9
2 models selected
> view matrix models
> #9,-0.76289,0.64653,0.00079928,171.76,-0.64641,-0.76278,0.017834,377.91,0.01214,0.013089,0.99984,7.3932
> view matrix models
> #9,-0.76289,0.64653,0.00079928,172.07,-0.64641,-0.76278,0.017834,377.35,0.01214,0.013089,0.99984,1.1369
> view matrix models
> #9,-0.76289,0.64653,0.00079928,170.39,-0.64641,-0.76278,0.017834,378.07,0.01214,0.013089,0.99984,1.5586
Fit map DS1_NTR_C_short_spike_reconstruction.mrc gaussian in map
short_better_spike_230505_reconstruction.mrc gaussian using 2828369 points
correlation = 0.9834, correlation about mean = 0.9158, overlap = 94.11
steps = 72, shift = 6.76, angle = 0.00662 degrees
Position of DS1_NTR_C_short_spike_reconstruction.mrc gaussian (#9) relative to
short_better_spike_230505_reconstruction.mrc gaussian (#7) coordinates:
Matrix rotation and translation
-0.76296394 0.64644053 0.00080189 171.56497894
-0.64632679 -0.76285184 0.01785303 380.68135233
0.01215265 0.01310293 0.99984029 7.67929719
Axis -0.00367420 -0.00877980 -0.99995471
Axis point 155.54265203 158.86058142 0.00000000
Rotation angle (degrees) 139.72830402
Shift along axis -11.65161969
> ~select #9
Nothing selected
> hide #!7 models
> color #9 #ff007f models transparency 0
> show #!14 models
> show #!20 models
> show #21 models
> hide #!20 models
> show #19 models
> color zone #9 near #14,19,21 distance 5
> hide #21 models
> hide #19 models
> lighting soft
> lighting simple
> hide #!9 models
> hide #!14 models
> show #!5.2 models
> volume gaussian #5.2 sDev 1.5
Opened DS1_NTR_C_others_spike_reconstruction.mrc gaussian as #11, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> hide #!5 models
> measure mapstats #11
Map DS1_NTR_C_others_spike_reconstruction.mrc gaussian #11, minimum -0.00432,
maximum 0.01484, mean 6.779e-05, SD 0.002155, RMS 0.002156
> volume #11 level 0.002156
> show #!8 models
> select #11
2 models selected
> view matrix models #11,1,0,0,137.97,0,1,0,78.693,0,0,1,24.461
> view matrix models #11,1,0,0,180.35,0,1,0,60.733,0,0,1,24.341
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.50733,0.86143,0.023643,280.22,-0.85257,-0.49774,-0.15928,448.6,-0.12544,-0.10096,0.98695,61.475
> view matrix models
> #11,-0.47641,0.87557,-0.080081,282.31,-0.8668,-0.48298,-0.12407,445.37,-0.14731,0.010307,0.98904,47.045
> view matrix models
> #11,-0.47863,0.8774,-0.032936,278.17,-0.87591,-0.47975,-0.051301,439.81,-0.060812,0.0042941,0.99814,33.469
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.47863,0.8774,-0.032936,94.563,-0.87591,-0.47975,-0.051301,378.71,-0.060812,0.0042941,0.99814,19.451
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.4763,0.87896,-0.023752,93.125,-0.87699,-0.47684,-0.059284,379.13,-0.063434,-0.0074072,0.99796,21.746
> view matrix models
> #11,-0.77698,0.62951,0.0040622,178.05,-0.62827,-0.77502,-0.06791,387.91,-0.039601,-0.055317,0.99768,25.617
Fit map DS1_NTR_C_others_spike_reconstruction.mrc gaussian in map
empty_spike_230505_reconstruction.mrc gaussian using 2782044 points
correlation = 0.9849, correlation about mean = 0.9173, overlap = 88.97
steps = 116, shift = 2.4, angle = 5.07 degrees
Position of DS1_NTR_C_others_spike_reconstruction.mrc gaussian (#11) relative
to empty_spike_230505_reconstruction.mrc gaussian (#8) coordinates:
Matrix rotation and translation
-0.76295098 0.64645588 0.00076323 171.56456886
-0.64634373 -0.76283959 0.01776301 380.68148429
0.01206522 0.01305900 0.99984193 7.69512160
Axis -0.00363846 -0.00874187 -0.99995517
Axis point 155.54487762 158.85972384 0.00000000
Rotation angle (degrees) 139.72711413
Shift along axis -11.64687581
> hide #!8 models
> ~select #11
Nothing selected
> color #11 #ff007f models transparency 0
> show #21 models
> show #19 models
> volume zone #11 nearAtoms #19,21 dis 5
Expected a keyword
> color zone #11 near #19,21 distance 5
> hide #21 models
> hide #19 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> lighting soft
> lighting simple
> save "C:/Users/yulab/Desktop/session 7-2024.7.26.cxs" includeMaps true
> lighting simple
> hide #!11 models
> show #!6 models
> lighting soft
> lighting simple
> view name 1
> view name 2
> hide #!6 models
> show #!7 models
> view list
Named views: 1, 2
> view 1
> view 2
> hide #!7 models
> show #!8 models
> view 2
> lighting soft
> lighting simple
> lighting soft
> view 2
> hide #!8 models
> show #!9 models
> view 2
> hide #!9 models
> show #!10 models
> view 2
> view 1
> view 2
> view 1
> view 2
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view name 3
> lighting simple
> lighting soft
> hide #!10 models
> show #!10 models
> view list
Named views: 1, 2, 3
> view 1
> view 2
> view 3
> view 2
> view 1
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view name 4
> hide #!10 models
> show #!11 models
> view list
Named views: 1, 2, 3, 4
> view 4
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!7 models
> lighting simple
> color zone #8 near #14,19,21,22 distance 5
> hide #!7 models
> hide #!8 models
> show #!7 models
> color zone #7 near #14,19,21,22 distance 5
> view 4
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view name 5
> hide #!7 models
> show #!8 models
> view list
Named views: 1, 2, 3, 4, 5
> view 5
> color zone #8 near #19,21,22 distance 5
> view 5
> hide #!8 models
> show #!6 models
> color zone #6 near #19-22 distance 5
> hide #!6 models
> show #!9 models
> view 5
[Repeated 1 time(s)]
> color zone #9 near #14,19,21 distance 5
> hide #!9 models
> show #!10 models
> view list
Named views: 1, 2, 3, 4, 5
> view 5
> hide #!10 models
> show #!11 models
> color zone #11 near #19,21 distance 5
> lighting simple
> hide #!11 models
> save "C:/Users/yulab/Desktop/session 8-2024.7.26.cxs" includeMaps true
——— End of log from Fri Jul 26 19:57:23 2024 ———
opened ChimeraX session
> open D:/DS1_TR_run_class001.mrc
Opened DS1_TR_run_class001.mrc as #16, grid size 288,288,288, pixel 1.06,
shown at level 0.0225, step 2, values float32
> volume gaussian #16 sDev 3
Opened DS1_TR_run_class001.mrc gaussian as #17, grid size 288,288,288, pixel
1.06, shown at step 1, values float32
> measure mapstats #17
Map DS1_TR_run_class001.mrc gaussian #17, minimum -0.003842, maximum 0.01021,
mean 0.0003218, SD 0.002151, RMS 0.002175
> volume #17 level 0.002175
> ui tool show "Side View"
> hide #!17 models
> show #!17 models
> color #17 #ff007f models transparency 0
> show #!20 models
> show #21 models
> show #!22 models
> show #19 models
> color zone #17 near #19-22 distance 5
> lighting simple
> hide #!17 models
> open D:/DS1_NTR_chymotrypsin_run_class001.mrc
Opened DS1_NTR_chymotrypsin_run_class001.mrc as #18, grid size 300,300,300,
pixel 1.06, shown at level 0.0168, step 2, values float32
> hide #19 models
> hide #!20 models
> hide #21 models
> hide #!22 models
> volume gaussian #18 sDev 3
Opened DS1_NTR_chymotrypsin_run_class001.mrc gaussian as #23, grid size
300,300,300, pixel 1.06, shown at step 1, values float32
> color #23 #ff007f models transparency 0
> measure mapstats #23
Map DS1_NTR_chymotrypsin_run_class001.mrc gaussian #23, minimum -0.002606,
maximum 0.008448, mean 0.0001781, SD 0.001823, RMS 0.001832
> volume #23 level 0.001832
> show #19 models
> show #!20 models
> show #21 models
> color zone #23 near #19-21 distance 5
> hide #19 models
> hide #!20 models
> hide #21 models
> show #!17 models
> select #23
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #23,1,0,0,-102.5,0,1,0,-110.33,0,0,1,-2.2603
> view matrix models #23,1,0,0,-105.01,0,1,0,-112.76,0,0,1,-2.4113
> view matrix models #23,1,0,0,-206.18,0,1,0,-218.41,0,0,1,7.5142
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.78693,0.61397,0.061507,-25.719,-0.61197,-0.78932,0.049617,158.62,0.079013,0.0014043,0.99687,-4.9664
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.78693,0.61397,0.061507,187.51,-0.61197,-0.78932,0.049617,359.02,0.079013,0.0014043,0.99687,-19.127
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.76485,0.64384,-0.021563,187.23,-0.63573,-0.74896,0.18683,343.2,0.10414,0.15661,0.98215,-46.388
> view matrix models
> #23,-0.76333,0.64565,-0.021581,186.7,-0.63752,-0.74747,0.18671,343.26,0.10442,0.15628,0.98218,-46.382
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.76333,0.64565,-0.021581,5.4934,-0.63752,-0.74747,0.18671,181.9,0.10442,0.15628,0.98218,-11.235
> view matrix models
> #23,-0.76333,0.64565,-0.021581,-48.894,-0.63752,-0.74747,0.18671,151.33,0.10442,0.15628,0.98218,-16.087
> view matrix models
> #23,-0.76333,0.64565,-0.021581,-88.295,-0.63752,-0.74747,0.18671,119.81,0.10442,0.15628,0.98218,-17.536
> view matrix models
> #23,-0.76333,0.64565,-0.021581,172.85,-0.63752,-0.74747,0.18671,346.58,0.10442,0.15628,0.98218,-30.354
> view matrix models
> #23,-0.76333,0.64565,-0.021581,173.28,-0.63752,-0.74747,0.18671,346.89,0.10442,0.15628,0.98218,-29.676
> ~select #23
Nothing selected
> ui tool show "Fit in Map"
Fit map DS1_NTR_chymotrypsin_run_class001.mrc gaussian in map
DS1_TR_run_class001.mrc gaussian using 3734585 points
correlation = 0.9807, correlation about mean = 0.8235, overlap = 65.31
steps = 168, shift = 14.9, angle = 9.98 degrees
Position of DS1_NTR_chymotrypsin_run_class001.mrc gaussian (#23) relative to
DS1_TR_run_class001.mrc gaussian (#17) coordinates:
Matrix rotation and translation
-0.76275757 0.64668364 0.00107206 171.48126031
-0.64659705 -0.76268060 0.01518399 380.70186467
0.01063688 0.01088851 0.99988414 7.31477901
Axis -0.00332127 -0.00739553 -0.99996714
Axis point 155.54508236 158.87605724 0.00000000
Rotation angle (degrees) 139.70962906
Shift along axis -10.69956787
> hide #!17 models
> show #21 models
> show #!20 models
> show #19 models
> color zone #23 near #19-21 distance 5
> hide #21 models
> hide #!20 models
> hide #19 models
> view list
Named views: 1, 2, 3, 4, 5
> view 5
> lighting soft
> color zone #23 near #19-21 distance 5
> save C:/Users/yulab/Desktop/中期图-2024.7.22/CR-分类.png width 1271 height 834
> supersample 3 transparentBackground true
> view list
Named views: 1, 2, 3, 4, 5
> view 4
> view 5
> view 4
> view 5
> hide #!23 models
> show #!17 models
> view 5
> view 4
[Repeated 1 time(s)]
> hide #!17 models
> show #!23 models
> view 4
> save C:/Users/yulab/Desktop/中期图-2024.7.22/CR-分类-2.png width 1271 height 834
> supersample 3 transparentBackground true
> hide #!23 models
> show #!17 models
> view 4
> save C:/Users/yulab/Desktop/中期图-2024.7.22/TR-分类-2.png width 1271 height 834
> supersample 3
> save C:/Users/yulab/Desktop/中期图-2024.7.22/TR-分类-3.png width 1271 height 834
> supersample 3 transparentBackground true
> lighting simple
> hide #!17 models
> show #!12 models
> select #12
15725 atoms, 16043 bonds, 6 pseudobonds, 1972 residues, 2 models selected
> ui tool show "Blast Protein"
Alignment identifier is 1
Alignment identifier is 12/E
> select clear
> select #12/C-D:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #12/C-D:1-12
196 atoms, 196 bonds, 24 residues, 1 model selected
> select #12/E:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:1-8
67 atoms, 67 bonds, 8 residues, 1 model selected
> select #12/E:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:1-520
2313 atoms, 2365 bonds, 1 pseudobond, 289 residues, 2 models selected
> select #12/E:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/E:2-13
96 atoms, 96 bonds, 12 residues, 1 model selected
> select #12/E:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:1-27
216 atoms, 218 bonds, 27 residues, 1 model selected
> select #12/E:260
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:260-280
188 atoms, 192 bonds, 21 residues, 1 model selected
> select #12/E:260
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/E:260-420
1281 atoms, 1315 bonds, 161 residues, 1 model selected
> select #12/E:259-260
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/E:259-572
2487 atoms, 2541 bonds, 314 residues, 1 model selected
> select #12/E:572-573
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #12/E:572-770
1350 atoms, 1367 bonds, 1 pseudobond, 169 residues, 2 models selected
> select #12/E:572-573
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #12/E:572-775
1390 atoms, 1407 bonds, 1 pseudobond, 174 residues, 2 models selected
> select #12/E:768
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/E:768-775
65 atoms, 64 bonds, 8 residues, 1 model selected
> hide #!12 models
> show #!22 models
> hide #!22 models
> show #!12 models
> select #12/C-D:3
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/C-D:3
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/C-D:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #12/C-D:1-13
208 atoms, 208 bonds, 26 residues, 1 model selected
> select #12/C-D:1-2
26 atoms, 24 bonds, 4 residues, 1 model selected
> select #12/C-D:1-2
26 atoms, 24 bonds, 4 residues, 1 model selected
> select #12/C-D:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #12/C-D:1-3
38 atoms, 36 bonds, 6 residues, 1 model selected
> select #12/C-D:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #12/C-D:1-86
1374 atoms, 1414 bonds, 172 residues, 1 model selected
> hide #!12 models
> show #!12 models
> select #12
15725 atoms, 16043 bonds, 6 pseudobonds, 1972 residues, 2 models selected
> ~select #12
Nothing selected
> hide #!12 models
> show #!22 models
> save C:/Users/yulab/Desktop/中期图-2024.7.22/Trypsin+VP7.png width 1271 height
> 834 supersample 3 transparentBackground true
> ui mousemode right "mark surface"
> ui mousemode right label
> hide #!22 models
> show #!12 models
> hide #!12 models
> show #!12 models
> show #!17 models
> lighting simple
> save C:/Users/yulab/Desktop/DS1-session/session-9-2024.8.17.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAB36E7400> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BACE1E2AC0>
'long_full_spike_230505_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BABF36E040>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAB36E7400> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BACE1E2AC0>
'long_full_spike_230505_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BABF36E040>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAB36E7400> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BACE1E2AC0>
'long_full_spike_230505_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BABF36E040>
ValueError: error processing: 'named views' -> -> -> 'surface' ->
'long_full_spike_230505_reconstruction.mrc' -> : Error while saving session
data for 'named views' -> -> -> 'surface' ->
'long_full_spike_230505_reconstruction.mrc' ->
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAB36E7400> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BACE1E2AC0>
'long_full_spike_230505_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BABF36E040>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAB36E7400> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BACE1E2AC0>
'long_full_spike_230505_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BABF36E040>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAB36E7400> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BACE1E2AC0>
'long_full_spike_230505_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BABF36E040>
ValueError: error processing: 'named views' -> -> -> 'surface' ->
'long_full_spike_230505_reconstruction.mrc' -> : Error while saving session
data for 'named views' -> -> -> 'surface' ->
'long_full_spike_230505_reconstruction.mrc' ->
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/yulab/Desktop/DS1-session/session 9-2024.8.17.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C37C0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C3070>
'empty_spike_230505_reconstruction.mrc' -> <chimerax.map.session.GridDataState
object at 0x000001BAD4D1A190>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C37C0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C3070>
'empty_spike_230505_reconstruction.mrc' -> <chimerax.map.session.GridDataState
object at 0x000001BAD4D1A190>: Error while saving session data for 'named
views' -> <chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40>
-> <chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C37C0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C3070>
'empty_spike_230505_reconstruction.mrc' -> <chimerax.map.session.GridDataState
object at 0x000001BAD4D1A190>
ValueError: error processing: 'named views' -> -> -> 'surface' ->
'empty_spike_230505_reconstruction.mrc' -> : Error while saving session data
for 'named views' -> -> -> 'surface' ->
'empty_spike_230505_reconstruction.mrc' ->
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C37C0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C3070>
'empty_spike_230505_reconstruction.mrc' -> <chimerax.map.session.GridDataState
object at 0x000001BAD4D1A190>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C37C0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C3070>
'empty_spike_230505_reconstruction.mrc' -> <chimerax.map.session.GridDataState
object at 0x000001BAD4D1A190>: Error while saving session data for 'named
views' -> <chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40>
-> <chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C37C0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C3070>
'empty_spike_230505_reconstruction.mrc' -> <chimerax.map.session.GridDataState
object at 0x000001BAD4D1A190>
ValueError: error processing: 'named views' -> -> -> 'surface' ->
'empty_spike_230505_reconstruction.mrc' -> : Error while saving session data
for 'named views' -> -> -> 'surface' ->
'empty_spike_230505_reconstruction.mrc' ->
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save F:/chimerax-session/DS1-session/2024.8.17.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.surface.cap.ClipCap object at 0x000001BAD18D6FA0> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C0A60> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C03D0>
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BAC994D520>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.surface.cap.ClipCap object at 0x000001BAD18D6FA0> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C0A60> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C03D0>
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BAC994D520>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.surface.cap.ClipCap object at 0x000001BAD18D6FA0> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C0A60> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C03D0>
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BAC994D520>
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface' ->
'DS1_NTR_C_long_spike_reconstruction.mrc' -> : Error while saving session data
for 'named views' -> -> -> 'cap far' -> 'surface' ->
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map\session.py", line 316, in state_from_grid_data
s['array'] = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.surface.cap.ClipCap object at 0x000001BAD18D6FA0> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C0A60> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C03D0>
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BAC994D520>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.surface.cap.ClipCap object at 0x000001BAD18D6FA0> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C0A60> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C03D0>
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BAC994D520>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BAD14F3F40> ->
<chimerax.std_commands.view.NamedView object at 0x000001BAD14F3C70> ->
<chimerax.surface.cap.ClipCap object at 0x000001BAD18D6FA0> 'cap far' ->
<chimerax.map.volume.VolumeSurface object at 0x000001BAD18C0A60> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BAD18C03D0>
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BAC994D520>
ValueError: error processing: 'named views' -> -> -> 'cap far' -> 'surface' ->
'DS1_NTR_C_long_spike_reconstruction.mrc' -> : Error while saving session data
for 'named views' -> -> -> 'cap far' -> 'surface' ->
'DS1_NTR_C_long_spike_reconstruction.mrc' ->
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 536.23
OpenGL renderer: NVIDIA GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 10SWCTO1WW
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 8,466,862,080
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving map in session |
comment:2 by , 14 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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Out of memory trying to copy a volume to a byte array to output into a session file. The user had 17 models opened. The machine has just 8 Gbytes of memory. Running Windows 10. Windows seems especially prone to out of memory errors.
If I get enough of these errors it might be worth putting some code in the most frequent places they happen while saving sessions to give the user a clearer error message saying they ran out of memory and might close some of the models especially volume models that have not been saved to separate files.