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Opened 4 years ago
Last modified 4 years ago
#6299 accepted defect
Region not in region_browser.sequence_regions
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab5-DL.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
416,416,416, pixel 0.858, shown at level 0.05, step 1, values float32
Log from Thu Mar 3 12:01:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\dahailuo\\\OneDrive - Nanyang Technological
> University\\\Temporal\\\202112_FlaviNS1\\\Data_EM_Alvin\\\20220302_D2NS1ts-
> Ab56-apoa1.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Wed Mar 2 00:18:18 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220302_D2NS1ts-
> Ab56-apoa1.cxs" format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Wed Mar 2 00:08:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Tue Feb 22 22:03:06 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56-AA1.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Tue Feb 22 21:54:19 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
352,352,352, pixel 0.85, shown at level 0.421, step 2, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
352,352,352, pixel 0.85, shown at level 0.471, step 1, values float32
Log from Tue Feb 22 21:05:12 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J91_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J91_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.0468, step 2, values float32
> surface dust #1 size 8.58
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #2, grid size
416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32
> surface dust #1 size 8.58
> surface dust #2 size 8.58
> close #2
> close #1
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J20_004_volume_map_sharp.mrc"
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 2, values float32
> surface dust #1 size 8.58
> surface dust #2 size 8.5
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/D2NS1.pdb"
Summary of feedback from opening D:/OneDrive - Nanyang Technological
University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
sNS1-Fab56-2/D2NS1.pdb
---
warning | Ignored bad PDB record found on line 5732
END
Chain information for D2NS1.pdb #3
---
Chain | Description
B C | No description available
> hide #!2 models
> volume #1 level 0.07524
> volume #1 level 0.07
> volume #1 level 0.072
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.89628,-0.44038,-0.052381,101.61,0.096778,0.078954,0.99217,-38.919,-0.43279,-0.89433,0.11338,384.44
> view matrix models
> #3,0.99109,-0.12056,-0.056551,31.91,0.0080432,0.4781,-0.87827,242.8,0.13292,0.86999,0.47482,-76.088
> view matrix models
> #3,0.79841,-0.57175,0.18879,97.95,-0.1953,0.050686,0.97943,19.471,-0.56956,-0.81886,-0.071196,428.68
> view matrix models
> #3,0.82022,-0.53629,0.19907,86.322,-0.4792,-0.8342,-0.2729,441.29,0.31242,0.12845,-0.94122,269.29
> view matrix models
> #3,0.33094,0.34033,0.88014,-96.351,-0.87516,0.45954,0.15137,217.82,-0.35295,-0.82036,0.44993,298
> view matrix models
> #3,0.12486,-0.10929,0.98614,-3.3941,-0.98525,0.10355,0.13622,299.73,-0.117,-0.9886,-0.094748,381.83
> view matrix models
> #3,-0.013734,0.34293,0.93926,-46.701,0.87722,0.45496,-0.15328,-35.332,-0.47989,0.82183,-0.30707,179.08
> view matrix models
> #3,-0.024741,-0.048477,0.99852,10.486,0.22627,0.97263,0.052827,-44.605,-0.97375,0.22725,-0.013095,313.53
> view matrix models
> #3,0.22803,-0.14862,0.96224,-10.67,-0.86757,-0.4796,0.13152,377.92,0.44195,-0.86481,-0.23831,288.28
> view matrix models
> #3,-0.090598,0.23885,0.96682,-20.594,-0.90644,0.38234,-0.1794,295.23,-0.4125,-0.89262,0.18187,368.38
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.090598,0.23885,0.96682,-20.895,-0.90644,0.38234,-0.1794,305.2,-0.4125,-0.89262,0.18187,368.62
> view matrix models
> #3,-0.090598,0.23885,0.96682,-18.453,-0.90644,0.38234,-0.1794,307.34,-0.4125,-0.89262,0.18187,380.09
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 72
shifted from previous position = 2.04
rotated from previous position = 4.6 degrees
atoms outside contour = 3319, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06802577 0.24460859 0.96723274 -24.08767794
-0.87342564 0.45395004 -0.17623011 287.61942533
-0.48218273 -0.85679405 0.18276711 387.90605974
Axis -0.34848182 0.74217118 -0.57248788
Axis point 265.32854097 -0.00000000 317.95880744
Rotation angle (degrees) 102.45391693
Shift along axis -0.21455122
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 40
shifted from previous position = 0.0168
rotated from previous position = 0.017 degrees
atoms outside contour = 3323, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06800908 0.24437415 0.96729317 -24.07786550
-0.87335170 0.45412951 -0.17613415 287.55836847
-0.48231900 -0.85676584 0.18253965 387.96533381
Axis -0.34851775 0.74227452 -0.57233199
Axis point 265.31869899 0.00000000 317.91033718
Rotation angle (degrees) 102.45483514
Shift along axis -0.20615891
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 44
shifted from previous position = 0.00415
rotated from previous position = 0.0128 degrees
atoms outside contour = 3322, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06778785 0.24439903 0.96730241 -24.12733834
-0.87337367 0.45415748 -0.17595301 287.52563608
-0.48231036 -0.85674392 0.18266531 387.93712068
Axis -0.34858450 0.74224338 -0.57233173
Axis point 265.33740374 0.00000000 317.91776063
Rotation angle (degrees) 102.44383763
Shift along axis -0.20430725
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 44
shifted from previous position = 0.0152
rotated from previous position = 0.013 degrees
atoms outside contour = 3321, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06797653 0.24451862 0.96725895 -24.09141306
-0.87335854 0.45410159 -0.17617224 287.57257739
-0.48231121 -0.85673942 0.18268417 387.93432608
Axis -0.34847884 0.74224049 -0.57239982
Axis point 265.31882258 -0.00000000 317.92823841
Rotation angle (degrees) 102.45045928
Shift along axis -0.21017795
> transparency #1.1 50
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/F562a.pdb"
Chain information for F562a.pdb #4
---
Chain | Description
B | No description available
C | No description available
> ui tool show "Color Actions"
> color sel bychain
> color sel bychain
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> color sel bychain
> color sel bychain
> color sel bychain
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/7bsc_DEN2 NS1c.pdb"
7bsc_DEN2 NS1c.pdb title:
Complex structure of 1G5.3 fab bound to DENV2 NS1C [more info...]
Chain information for 7bsc_DEN2 NS1c.pdb #5
---
Chain | Description
A | non-structural protein 1
H | 1G5.3 fab heavy chain
L | 1G5.3 fab light chain
> mmaker #5 to #3
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 D2NS1.pdb, chain B (#3) with 7bsc_DEN2 NS1c.pdb, chain A (#5),
sequence alignment score = 896.9
RMSD between 162 pruned atom pairs is 0.535 angstroms; (across all 177 pairs:
2.714)
> mmaker #4 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7bsc_DEN2 NS1c.pdb, chain H (#5) with F562a.pdb, chain B (#4),
sequence alignment score = 1028.9
RMSD between 105 pruned atom pairs is 0.627 angstroms; (across all 215 pairs:
11.308)
> ~select #4
Nothing selected
> hide #!5 models
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #4,0.59089,-0.15644,-0.79144,253.32,0.26071,0.96541,0.0038114,-36.876,0.76347,-0.20859,0.61123,8.3612
> view matrix models
> #4,0.59089,-0.15644,-0.79144,249.54,0.26071,0.96541,0.0038114,-38.171,0.76347,-0.20859,0.61123,-6.5674
> view matrix models
> #4,0.59089,-0.15644,-0.79144,250.18,0.26071,0.96541,0.0038114,-52.258,0.76347,-0.20859,0.61123,-8.7931
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.08302, steps = 284
shifted from previous position = 3.86
rotated from previous position = 9.32 degrees
atoms outside contour = 2026, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.70756240 -0.18104725 -0.68306467 216.74116501
0.24257753 0.97011437 -0.00585274 -48.06381473
0.66371047 -0.16155497 0.73033445 -11.10097449
Axis -0.10961944 -0.94817357 0.29824565
Axis point 132.17662306 0.00000000 263.68811665
Rotation angle (degrees) 45.25073566
Shift along axis 18.50297639
> transparency #1.1 0
> view matrix models
> #4,0.70756,-0.18105,-0.68306,218.9,0.24258,0.97011,-0.0058527,-47.556,0.66371,-0.16155,0.73033,-11.137
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.60929,0.056492,-0.79093,206.86,0.79214,-0.088481,0.60389,-30.096,-0.035867,-0.99447,-0.09866,369.53
> view matrix models
> #4,0.13536,-0.077461,-0.98776,343.37,0.97999,0.15727,0.12197,-53.095,0.1459,-0.98451,0.097201,310.49
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 96
shifted from previous position = 8.35
rotated from previous position = 5.73 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18515527 -0.12030538 -0.97531746 334.84540290
0.98054878 0.08839233 0.17524520 -44.47549541
0.06512764 -0.98879392 0.13433160 327.48525231
Axis -0.60933659 -0.54463915 0.57626133
Axis point 0.00000000 23.05515362 346.04002443
Rotation angle (degrees) 107.22113422
Shift along axis 8.90662490
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 28
shifted from previous position = 0.017
rotated from previous position = 0.0169 degrees
atoms outside contour = 1608, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18543237 -0.12023134 -0.97527394 334.76776945
0.98049261 0.08847529 0.17551742 -44.49851310
0.06518495 -0.98879550 0.13429212 327.47372226
Axis -0.60944823 -0.54461805 0.57616320
Axis point 0.00000000 23.10963968 345.96113737
Rotation angle (degrees) 107.21151966
Shift along axis 8.88937821
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 44
shifted from previous position = 0.0205
rotated from previous position = 0.0218 degrees
atoms outside contour = 1604, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18554107 -0.12011878 -0.97526714 334.73699226
0.98049338 0.08814571 0.17567888 -44.47566373
0.06486328 -0.98883862 0.13413032 327.56427605
Axis -0.60959315 -0.54447990 0.57614045
Axis point 0.00000000 23.17721063 345.92539580
Rotation angle (degrees) 107.22299700
Shift along axis 8.88575635
> transparency #1.1 50
> view matrix models
> #4,0.95986,-0.22484,0.16768,73.526,0.27579,0.64758,-0.71034,90.606,0.051126,0.72807,0.68359,-47.104
> view matrix models
> #4,0.75847,0.64831,0.066474,-35.582,0.26049,-0.20809,-0.94278,276.59,-0.59738,0.73239,-0.32671,193.1
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.09049, steps = 88
shifted from previous position = 2.42
rotated from previous position = 6.19 degrees
atoms outside contour = 1911, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72637414 0.68694818 -0.02197301 -24.03798979
0.18664733 -0.22792648 -0.95562142 294.38643021
-0.66147062 0.69003748 -0.29377694 209.53189487
Axis 0.89678670 0.34848835 -0.27263435
Axis point 0.00000000 72.78629578 205.81231454
Rotation angle (degrees) 113.43226483
Shift along axis 23.90769923
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0905, steps = 44
shifted from previous position = 0.0137
rotated from previous position = 0.0204 degrees
atoms outside contour = 1906, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72623985 0.68709241 -0.02190190 -24.03578291
0.18654834 -0.22764140 -0.95570869 294.36480593
-0.66164597 0.68998798 -0.29349821 209.53312556
Axis 0.89671635 0.34858730 -0.27273923
Axis point 0.00000000 72.74870511 205.83733915
Rotation angle (degrees) 113.41885466
Shift along axis 23.91065009
> view matrix models
> #4,0.4777,0.81916,-0.31746,33.473,0.28288,-0.48553,-0.82719,308.03,-0.83173,0.30535,-0.46366,331.51
> view matrix models
> #4,0.53443,0.7221,-0.43927,54.882,0.15416,-0.59427,-0.78935,347.48,-0.83104,0.35413,-0.42891,318.4
> view matrix models
> #4,0.55861,0.65321,-0.51116,71.372,0.070767,-0.65156,-0.75529,369.52,-0.82641,0.38574,-0.41019,309.57
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 104
shifted from previous position = 3.1
rotated from previous position = 2.07 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58731938 0.63730986 -0.49889086 69.51709433
0.06189895 -0.64996950 -0.75743526 371.85473470
-0.80698480 0.41397558 -0.42118849 304.38816914
Axis 0.87354940 0.22975311 -0.42909784
Axis point 0.00000000 108.25389938 250.40641939
Rotation angle (degrees) 137.89516888
Shift along axis 15.54909083
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 100
shifted from previous position = 0.0102
rotated from previous position = 0.0178 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58732049 0.63712467 -0.49912604 69.58840441
0.06165901 -0.65012663 -0.75731997 371.91413492
-0.80700236 0.41401391 -0.42111716 304.37603978
Axis 0.87355306 0.22960687 -0.42916866
Axis point 0.00000000 108.28874120 250.42594564
Rotation angle (degrees) 137.89878759
Shift along axis 15.55454641
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 84
shifted from previous position = 0.011
rotated from previous position = 0.0172 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58733885 0.63729229 -0.49889038 69.51578518
0.06188954 -0.64997620 -0.75743028 371.85701767
-0.80697135 0.41399213 -0.42119800 304.38350057
Axis 0.87355567 0.22974281 -0.42909059
Axis point 0.00000000 108.25696578 250.40359329
Rotation angle (degrees) 137.89502914
Shift along axis 15.54928904
> view matrix models
> #4,0.65819,-0.32045,-0.68124,252,0.74547,0.15105,0.6492,-68.256,-0.10513,-0.93515,0.3383,328.44
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.102, steps = 172
shifted from previous position = 4.22
rotated from previous position = 10.1 degrees
atoms outside contour = 1745, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62980729 -0.32213914 -0.70680207 259.21419516
0.77615676 0.29659722 0.55642680 -86.34491343
0.03038868 -0.89903085 0.43682956 282.25072430
Axis -0.74003611 -0.37482903 0.55843509
Axis point 0.00000000 121.16366768 309.58820660
Rotation angle (degrees) 79.53603811
Shift along axis -1.84457671
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0802
rotated from previous position = 0.389 degrees
atoms outside contour = 1748, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62493642 -0.32416938 -0.71018919 260.92042942
0.78000765 0.29690303 0.55085085 -86.37873091
0.03228835 -0.89819976 0.43840012 281.55642716
Axis -0.73657217 -0.37741145 0.56126823
Axis point 0.00000000 119.97837519 311.01534570
Rotation angle (degrees) 79.62326298
Shift along axis -1.55772605
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 44
shifted from previous position = 0.00561
rotated from previous position = 0.0322 degrees
atoms outside contour = 1746, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62451536 -0.32441238 -0.71044858 261.07250560
0.78034368 0.29682398 0.55041736 -86.36985039
0.03231597 -0.89813815 0.43852428 281.52393140
Axis -0.73629476 -0.37754414 0.56154292
Axis point 0.00000000 119.89834457 311.14057931
Rotation angle (degrees) 79.63421202
Shift along axis -1.53011648
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 80
shifted from previous position = 0.189
rotated from previous position = 1.07 degrees
atoms outside contour = 1750, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61106207 -0.33151468 -0.71881930 265.86650256
0.79073980 0.29753498 0.53497991 -86.41685086
0.03652019 -0.89530496 0.44395419 279.51480621
Axis -0.72651910 -0.38367781 0.57005380
Axis point 0.00000000 116.77430340 315.34054751
Rotation angle (degrees) 79.84710044
Shift along axis -0.66238880
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 60
shifted from previous position = 0.014
rotated from previous position = 0.0403 degrees
atoms outside contour = 1749, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61056528 -0.33194773 -0.71904155 266.05161554
0.79112724 0.29741686 0.53447255 -86.39981112
0.03643813 -0.89518374 0.44420530 279.47442312
Axis -0.72617579 -0.38373633 0.57045170
Axis point 0.00000000 116.70216550 315.50779421
Rotation angle (degrees) 79.85768786
Shift along axis -0.61883651
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 56
shifted from previous position = 0.00922
rotated from previous position = 0.0302 degrees
atoms outside contour = 1747, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61096453 -0.33178461 -0.71877766 265.91505542
0.79082389 0.29745317 0.53490111 -86.40973158
0.03633074 -0.89523215 0.44411653 279.51627475
Axis -0.72644097 -0.38355984 0.57023274
Axis point -0.00000000 116.79213793 315.39803173
Rotation angle (degrees) 79.84759520
Shift along axis -0.63895706
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 60
shifted from previous position = 0.0112
rotated from previous position = 0.0392 degrees
atoms outside contour = 1755, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61092141 -0.33119723 -0.71908514 265.86201413
0.79084444 0.29729954 0.53495614 -86.39268360
0.03660768 -0.89550063 0.44355214 279.58799940
Axis -0.72655505 -0.38383015 0.56990540
Axis point 0.00000000 116.72048670 315.29183470
Rotation angle (degrees) 79.86974659
Shift along axis -0.66456157
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0123
rotated from previous position = 0.0779 degrees
atoms outside contour = 1747, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61046660 -0.33218219 -0.71901706 266.11491018
0.79119095 0.29782655 0.53415002 -86.45092816
0.03670725 -0.89496053 0.44463270 279.33262127
Axis -0.72594735 -0.38388637 0.57064148
Axis point 0.00000000 116.64464322 315.61501173
Rotation angle (degrees) 79.83619740
Shift along axis -0.59930216
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 36
shifted from previous position = 0.00553
rotated from previous position = 0.0185 degrees
atoms outside contour = 1746, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61052405 -0.33197184 -0.71906543 266.07628678
0.79114928 0.29764543 0.53431266 -86.42628442
0.03664978 -0.89509882 0.44435898 279.40085187
Axis -0.72607396 -0.38386786 0.57049283
Axis point 0.00000000 116.66062451 315.54721201
Rotation angle (degrees) 79.84776315
Shift along axis -0.61860883
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0181
rotated from previous position = 0.0284 degrees
atoms outside contour = 1749, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61082613 -0.33169276 -0.71893766 265.95113585
0.79091989 0.29755592 0.53470198 -86.43037190
0.03656738 -0.89523203 0.44409733 279.47798684
Axis -0.72633614 -0.38375939 0.57023200
Axis point -0.00000000 116.71858763 315.43181746
Rotation angle (degrees) 79.84919126
Shift along axis -0.63416214
> view matrix models
> #4,0.4439,-0.28201,-0.85054,303.77,0.88884,0.018251,0.45784,-44.907,-0.11359,-0.95924,0.25876,341.18
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 424
shifted from previous position = 2.2
rotated from previous position = 6.39 degrees
atoms outside contour = 1635, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47014986 -0.27680804 -0.83805515 296.29282889
0.88242695 0.12936746 0.45231266 -60.98673857
-0.01678672 -0.95217718 0.30508496 317.15529629
Axis -0.70304515 -0.41110215 0.58027799
Axis point 0.00000000 97.60706796 321.98215187
Rotation angle (degrees) 92.73398070
Shift along axis 0.80277942
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 44
shifted from previous position = 0.0281
rotated from previous position = 0.296 degrees
atoms outside contour = 1634, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47131282 -0.27849458 -0.83684228 296.21168106
0.88186020 0.13410185 0.45203904 -61.71403302
-0.01366832 -0.95102969 0.30879721 315.93242787
Axis -0.70218063 -0.41196614 0.58071186
Axis point 0.00000000 97.40904882 322.29816415
Rotation angle (degrees) 92.45840264
Shift along axis 0.89569574
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.16 degrees
atoms outside contour = 1637, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47202347 -0.27915399 -0.83622180 296.12646474
0.88150690 0.13674791 0.45193539 -62.12511633
-0.01180798 -0.95045940 0.31062439 315.27843547
Axis -0.70176755 -0.41254208 0.58080232
Axis point 0.00000000 97.28028496 322.43137386
Rotation angle (degrees) 92.30976635
Shift along axis 0.93172962
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 40
shifted from previous position = 0.0221
rotated from previous position = 0.193 degrees
atoms outside contour = 1638, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47308077 -0.28050864 -0.83517034 296.03384583
0.88096007 0.13964438 0.45211592 -62.58112928
-0.01019558 -0.94963907 0.31317998 314.52160203
Axis -0.70135897 -0.41277074 0.58113330
Axis point 0.00000000 97.26838533 322.61659552
Rotation angle (degrees) 92.12314752
Shift along axis 0.98464198
> transparency #1.1 0
> view matrix models
> #4,0.84021,-0.0035817,-0.54224,142.19,-0.39021,0.69038,-0.60919,201.03,0.37654,0.72344,0.57867,-93.731
> view matrix models
> #4,0.79315,-0.11192,-0.59866,177.39,0.50761,-0.42168,0.75135,74.2,-0.33653,-0.89981,-0.27764,436.47
> view matrix models
> #4,0.7358,0.3335,-0.58938,106.02,-0.64815,0.094684,-0.7556,375.07,-0.19619,0.93798,0.28583,9.2542
> view matrix models
> #4,0.79115,-0.59673,-0.13416,211.08,0.60994,0.75351,0.24535,-98.992,-0.045318,-0.27593,0.96011,122.12
> view matrix models
> #4,0.66555,-0.4336,-0.60749,260.88,0.69641,0.65352,0.29652,-103.07,0.26843,-0.62041,0.73691,152.31
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1, steps = 416
shifted from previous position = 2.7
rotated from previous position = 17.5 degrees
atoms outside contour = 1774, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67732915 -0.28469604 -0.67836083 239.91883502
0.71088577 0.49065254 0.50388643 -103.74543128
0.18938499 -0.82353401 0.53471962 227.48787848
Axis -0.70890735 -0.46341865 0.53168931
Axis point 0.00000000 101.86597662 309.82596584
Rotation angle (degrees) 69.43005060
Shift along axis -1.04978373
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1, steps = 44
shifted from previous position = 0.00594
rotated from previous position = 0.0194 degrees
atoms outside contour = 1776, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67756361 -0.28454385 -0.67819052 239.83133941
0.71064745 0.49081816 0.50406126 -103.75597407
0.18944069 -0.82348792 0.53477088 227.46549023
Axis -0.70904026 -0.46339937 0.53152886
Axis point 0.00000000 101.90886125 309.76335536
Rotation angle (degrees) 69.41623953
Shift along axis -1.06514982
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.09997, steps = 40
shifted from previous position = 0.0133
rotated from previous position = 0.00996 degrees
atoms outside contour = 1778, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67763562 -0.28462709 -0.67808363 239.81516361
0.71058849 0.49090368 0.50406111 -103.75178064
0.18940430 -0.82340817 0.53490655 227.43306000
Axis -0.70903930 -0.46335011 0.53157309
Axis point 0.00000000 101.93201901 309.76345143
Rotation angle (degrees) 69.40726713
Shift along axis -1.06768104
> view matrix models
> #4,0.67386,0.21665,-0.70638,152.68,-0.73712,0.13162,-0.66282,370.99,-0.050625,0.96733,0.2484,-19.457
> view matrix models
> #4,0.26977,0.74198,-0.61375,121.96,-0.64983,-0.33008,-0.68467,441.19,-0.7106,0.58353,0.39312,157.04
> view matrix models
> #4,0.83537,0.35405,-0.42048,63.612,-0.53507,0.34852,-0.76957,306.25,-0.12592,0.86786,0.48059,-14.673
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1062, steps = 108
shifted from previous position = 1.02
rotated from previous position = 11.1 degrees
atoms outside contour = 1639, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88907475 0.29063713 -0.35366111 56.95234558
-0.45699328 0.51877555 -0.72251581 256.52548266
-0.02651919 0.80399130 0.59404945 -35.16228912
Axis 0.88188843 -0.18899530 -0.43191847
Axis point 0.00000000 161.74872048 251.74241852
Rotation angle (degrees) 59.93713751
Shift along axis 16.93074519
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1062, steps = 44
shifted from previous position = 0.0122
rotated from previous position = 0.077 degrees
atoms outside contour = 1637, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88924092 0.29042756 -0.35341541 56.93133633
-0.45670512 0.51991995 -0.72187513 256.18534624
-0.02590471 0.80332752 0.59497383 -35.27785394
Axis 0.88179482 -0.18935008 -0.43195422
Axis point -0.00000000 161.74523741 251.76190662
Rotation angle (degrees) 59.86313127
Shift along axis 16.93146051
> view matrix models
> #4,0.83879,0.21495,-0.50022,97.467,-0.52296,0.062549,-0.85006,366.96,-0.15144,0.97462,0.16488,7.9202
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1097, steps = 264
shifted from previous position = 0.803
rotated from previous position = 13.4 degrees
atoms outside contour = 1566, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.90125965 0.23249395 -0.36561951 66.81826163
-0.42074684 0.26813163 -0.86664730 312.38684742
-0.10345610 0.93490749 0.33947732 -14.03685609
Axis 0.93143071 -0.13554240 -0.33773523
Axis point 0.00000000 165.03559591 224.93775063
Rotation angle (degrees) 75.25993272
Shift along axis 24.63566001
> view matrix models
> #4,0.85035,0.35218,-0.39099,57.593,-0.48265,0.22596,-0.84616,329.25,-0.20965,0.90825,0.36212,8.0544
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85035,0.35218,-0.39099,60.231,-0.48265,0.22596,-0.84616,326.26,-0.20965,0.90825,0.36212,12.759
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 168
shifted from previous position = 2.33
rotated from previous position = 5.98 degrees
atoms outside contour = 1596, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88028089 0.25385290 -0.40082949 74.19694561
-0.45618497 0.22068248 -0.86208731 322.45385437
-0.13038732 0.94173137 0.31006645 -3.17418883
Axis 0.92158142 -0.13817047 -0.36276246
Axis point 0.00000000 162.85511452 230.82234394
Rotation angle (degrees) 78.14035717
Shift along axis 24.97640109
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.011
rotated from previous position = 0.0221 degrees
atoms outside contour = 1600, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88011312 0.25412437 -0.40102585 74.19170998
-0.45646647 0.22069435 -0.86193525 322.48434036
-0.13053461 0.94165537 0.31023525 -3.15440043
Axis 0.92146618 -0.13819573 -0.36304548
Axis point 0.00000000 162.86097718 230.89097488
Rotation angle (degrees) 78.13997962
Shift along axis 24.94438268
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.00421
rotated from previous position = 0.0136 degrees
atoms outside contour = 1600, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88018838 0.25419012 -0.40081894 74.13944294
-0.45629950 0.22079847 -0.86199700 322.44263683
-0.13061091 0.94161321 0.31033107 -3.14778151
Axis 0.92150340 -0.13805512 -0.36300449
Axis point 0.00000000 162.82540766 230.87431985
Rotation angle (degrees) 78.13192347
Shift along axis 24.94755119
> view matrix models
> #4,0.88019,0.25419,-0.40082,73.448,-0.4563,0.2208,-0.862,321.07,-0.13061,0.94161,0.31033,-5.8994
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 160
shifted from previous position = 2.99
rotated from previous position = 8.44 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87327534 0.17162879 -0.45599755 97.28727310
-0.48720393 0.31672140 -0.81383039 304.58441441
0.00474745 0.93286180 0.36020320 -32.68286674
Axis 0.90839597 -0.23961801 -0.34263678
Axis point 0.00000000 182.33141527 229.00675692
Rotation angle (degrees) 74.03202850
Shift along axis 26.58980844
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 80
shifted from previous position = 0.0187
rotated from previous position = 0.0503 degrees
atoms outside contour = 1606, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87307788 0.17102576 -0.45660182 97.51562460
-0.48755025 0.31670719 -0.81362849 304.62173537
0.00545764 0.93297736 0.35989370 -32.78455753
Axis 0.90828067 -0.24028299 -0.34247673
Axis point 0.00000000 182.48861826 229.00019788
Rotation angle (degrees) 74.04755731
Shift along axis 26.60408358
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 64
shifted from previous position = 0.00983
rotated from previous position = 0.00562 degrees
atoms outside contour = 1605, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87308357 0.17093159 -0.45662622 97.52642834
-0.48753906 0.31671935 -0.81363046 304.61327140
0.00554721 0.93299049 0.35985828 -32.79571036
Axis 0.90828615 -0.24034163 -0.34242104
Axis point 0.00000000 182.49871036 228.98437979
Rotation angle (degrees) 74.04808080
Shift along axis 26.60059602
> ui mousemode right "rotate selected models"
> transparency #1.1 50
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.87308,0.17093,-0.45663,98.781,-0.48754,0.31672,-0.81363,307.95,0.0055472,0.93299,0.35986,-31.624
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1045, steps = 152
shifted from previous position = 1.66
rotated from previous position = 10.1 degrees
atoms outside contour = 1670, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85430945 0.22816829 -0.46700601 94.00588935
-0.50530889 0.15416741 -0.84905556 345.08239658
-0.12173045 0.96133847 0.24700214 -1.12292161
Axis 0.91267386 -0.17406375 -0.36976782
Axis point 0.00000000 176.18270876 236.27702715
Rotation angle (degrees) 82.66101368
Shift along axis 26.14560144
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1045, steps = 60
shifted from previous position = 0.00837
rotated from previous position = 0.0183 degrees
atoms outside contour = 1667, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85416080 0.22824487 -0.46724044 94.04888675
-0.50553655 0.15397090 -0.84895570 345.14108146
-0.12182835 0.96135179 0.24690203 -1.09962552
Axis 0.91260386 -0.17412755 -0.36991051
Axis point 0.00000000 176.20594034 236.31033169
Rotation angle (degrees) 82.67387511
Shift along axis 26.13756946
> view matrix models
> #4,0.85416,0.22824,-0.46724,92.304,-0.50554,0.15397,-0.84896,343.85,-0.12183,0.96135,0.2469,-1.3966
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 132
shifted from previous position = 2.46
rotated from previous position = 10.1 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87327321 0.17148581 -0.45605541 97.32164807
-0.48720576 0.31684479 -0.81378127 304.55640572
0.00494684 0.93284619 0.36024093 -32.71905415
Axis 0.90838381 -0.23975747 -0.34257148
Axis point 0.00000000 182.35784967 228.99751317
Rotation angle (degrees) 74.02729082
Shift along axis 26.59434986
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 100
shifted from previous position = 0.0199
rotated from previous position = 0.0492 degrees
atoms outside contour = 1607, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87291436 0.17135958 -0.45678926 97.50396396
-0.48784609 0.31650499 -0.81352984 304.69020219
0.00516995 0.93298473 0.35987885 -32.73221582
Axis 0.90818184 -0.24021727 -0.34278478
Axis point 0.00000000 182.47945606 229.06508608
Rotation angle (degrees) 74.05889597
Shift along axis 26.57958591
> volume #1 step 1
> volume #1 level 0.08
> volume #2 step 1
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 96
shifted from previous position = 0.0269
rotated from previous position = 0.0588 degrees
atoms outside contour = 1705, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87339018 0.17133657 -0.45588748 97.30726750
-0.48699588 0.31678456 -0.81393032 304.55388891
0.00496208 0.93289407 0.36011672 -32.71648369
Axis 0.90847710 -0.23967565 -0.34238127
Axis point 0.00000000 182.34480224 228.95151912
Rotation angle (degrees) 74.02930115
Shift along axis 26.60878416
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 60
shifted from previous position = 0.0234
rotated from previous position = 0.0504 degrees
atoms outside contour = 1711, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87307658 0.17097372 -0.45662380 97.51998587
-0.48755237 0.31664803 -0.81365025 304.63116274
0.00547621 0.93300698 0.35981662 -32.78056504
Axis 0.90828882 -0.24029916 -0.34244377
Axis point 0.00000000 182.49216804 228.98849803
Rotation angle (degrees) 74.05165523
Shift along axis 26.59919907
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 84
shifted from previous position = 0.0236
rotated from previous position = 0.0512 degrees
atoms outside contour = 1709, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87330072 0.17150987 -0.45599367 97.31366850
-0.48715626 0.31696366 -0.81376461 304.52650710
0.00496476 0.93280138 0.36035670 -32.73218629
Axis 0.90838730 -0.23974404 -0.34257162
Axis point 0.00000000 182.35082823 229.00016180
Rotation angle (degrees) 74.01947881
Shift along axis 26.60320358
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 36
shifted from previous position = 0.0101
rotated from previous position = 0.0146 degrees
atoms outside contour = 3383, contour level = 0.08
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06781116 0.24433459 0.96731706 -24.10970616
-0.87336663 0.45417416 -0.17594486 287.52120019
-0.48231982 -0.85675345 0.18259559 387.95373087
Axis -0.34859656 0.74226213 -0.57230007
Axis point 265.34079550 0.00000000 317.90521257
Rotation angle (degrees) 102.44607735
Shift along axis -0.20528738
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 40
shifted from previous position = 0.00617
rotated from previous position = 0.0174 degrees
atoms outside contour = 3388, contour level = 0.08
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06800223 0.24456045 0.96724657 -24.09574276
-0.87334229 0.45411451 -0.17621946 287.57652794
-0.48233700 -0.85672063 0.18270418 387.93151574
Axis -0.34844475 0.74224675 -0.57241245
Axis point 265.30857487 0.00000000 317.93174566
Rotation angle (degrees) 102.45024724
Shift along axis -0.20805003
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.8783,0.21948,-0.42476,83.959,-0.47606,0.31931,-0.81939,302.68,-0.044211,0.92188,0.38494,-24.427
> view matrix models
> #4,0.88185,0.18737,-0.43271,90.075,-0.47057,0.40846,-0.78213,281.03,0.030198,0.89334,0.44837,-40.684
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 108
shifted from previous position = 0.192
rotated from previous position = 5.8 degrees
atoms outside contour = 1706, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87316782 0.17153805 -0.45623751 97.35347505
-0.48739404 0.31688450 -0.81365305 304.56284709
0.00500214 0.93282310 0.36029997 -32.73417130
Axis 0.90830421 -0.23988070 -0.34269623
Axis point 0.00000000 182.38522859 229.02890887
Rotation angle (degrees) 74.02748836
Shift along axis 26.58569939
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 100
shifted from previous position = 0.0157
rotated from previous position = 0.0308 degrees
atoms outside contour = 1714, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87319228 0.17106442 -0.45636852 97.46138911
-0.48734683 0.31669009 -0.81375701 304.60534678
0.00532251 0.93297608 0.35989904 -32.76360108
Axis 0.90836070 -0.24009506 -0.34239627
Axis point 0.00000000 182.44525999 228.97324319
Rotation angle (degrees) 74.04449916
Shift along axis 26.61399150
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 76
shifted from previous position = 0.0215
rotated from previous position = 0.0496 degrees
atoms outside contour = 1707, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87344661 0.17154945 -0.45569927 97.23463453
-0.48689717 0.31676739 -0.81399606 304.54231699
0.00471009 0.93286078 0.36020634 -32.68225206
Axis 0.90851141 -0.23945131 -0.34244721
Axis point 0.00000000 182.29150588 228.95203805
Rotation angle (degrees) 74.02546087
Shift along axis 26.60766517
> close #5
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb"
Chain information for F562b.pdb #5
---
Chain | Description
B | No description available
C | No description available
> select #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,0.88246,-0.46571,0.066244,91.139,0.4452,0.87234,0.20206,-101.84,-0.15189,-0.14881,0.97713,59.494
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.88246,-0.46571,0.066244,31.321,0.4452,0.87234,0.20206,-110.9,-0.15189,-0.14881,0.97713,2.868
> view matrix models
> #5,0.88246,-0.46571,0.066244,29.937,0.4452,0.87234,0.20206,-111.7,-0.15189,-0.14881,0.97713,-4.3706
> view matrix models
> #5,0.91945,-0.24365,-0.30863,71.496,-0.34812,-0.86933,-0.35081,481.22,-0.18283,0.42999,-0.88413,336.53
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1014, steps = 252
shifted from previous position = 4.97
rotated from previous position = 12.4 degrees
atoms outside contour = 1810, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.96186420 -0.19777272 -0.18895294 31.32789418
-0.26901427 -0.80896731 -0.52268846 497.86596548
-0.04948323 0.55358635 -0.83132038 280.55853441
Axis 0.98957826 -0.12823509 -0.06550286
Axis point 0.00000000 209.55045747 214.71270936
Rotation angle (degrees) 147.05697484
Shift along axis -51.21986933
> view matrix models
> #5,0.96186,-0.19777,-0.18895,31.586,-0.26901,-0.80897,-0.52269,497.84,-0.049483,0.55359,-0.83132,280.45
> view matrix models
> #5,0.96186,-0.19777,-0.18895,30.409,-0.26901,-0.80897,-0.52269,498.49,-0.049483,0.55359,-0.83132,281.14
> view matrix models
> #5,0.88111,-0.30725,-0.35949,105.37,-0.46365,-0.71093,-0.52878,515.6,-0.093104,0.63259,-0.76887,259.2
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 80
shifted from previous position = 3.4
rotated from previous position = 5.08 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88807867 -0.23238898 -0.39662534 101.69393944
-0.43540490 -0.70196949 -0.56361460 519.59851714
-0.14744106 0.67322671 -0.72458742 250.51818794
Axis 0.96785351 -0.19499177 -0.15886409
Axis point 0.00000000 224.56879044 228.99496698
Rotation angle (degrees) 140.28561169
Shift along axis -42.69094177
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0247
rotated from previous position = 0.0823 degrees
atoms outside contour = 1771, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88749875 -0.23316934 -0.39746451 102.13143422
-0.43663025 -0.70123937 -0.56357554 519.69347155
-0.14730923 0.67371761 -0.72415784 250.30786189
Axis 0.96767878 -0.19564479 -0.15912543
Axis point 0.00000000 224.69705024 229.03906748
Rotation angle (degrees) 140.25962425
Shift along axis -42.67524524
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0089
rotated from previous position = 0.0313 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88726809 -0.23348649 -0.39779316 102.30830437
-0.43710961 -0.70099140 -0.56351243 519.72597500
-0.14727705 0.67386581 -0.72402648 250.24321586
Axis 0.96761002 -0.19589960 -0.15923003
Axis point 0.00000000 224.74651301 229.05595353
Rotation angle (degrees) 140.25296234
Shift along axis -42.66580653
> view matrix models
> #5,0.90434,-0.19289,-0.38074,87.744,-0.3816,-0.76498,-0.51883,511.31,-0.19118,0.61449,-0.76541,278.75
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 100
shifted from previous position = 0.228
rotated from previous position = 5.49 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88741151 -0.23323538 -0.39762052 102.19303295
-0.43675670 -0.70132020 -0.56337694 519.68635289
-0.14745987 0.67361061 -0.72422672 250.37123988
Axis 0.96765550 -0.19569262 -0.15920817
Axis point 0.00000000 224.70331960 229.05340664
Rotation angle (degrees) 140.27024302
Shift along axis -42.67227987
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 80
shifted from previous position = 0.0119
rotated from previous position = 0.0244 degrees
atoms outside contour = 1769, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88757691 -0.23309386 -0.39733424 102.06718757
-0.43649500 -0.70124393 -0.56367462 519.68560309
-0.14723913 0.67373898 -0.72415222 250.29116827
Axis 0.96770087 -0.19558315 -0.15906683
Axis point 0.00000000 224.68268474 229.02792313
Rotation angle (degrees) 140.25607412
Shift along axis -42.68426633
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 64
shifted from previous position = 0.0443
rotated from previous position = 0.146 degrees
atoms outside contour = 1761, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88644690 -0.23468134 -0.39891925 102.92117215
-0.43878232 -0.70033958 -0.56302270 519.80857088
-0.14724801 0.67412844 -0.72378787 250.13865633
Axis 0.96736944 -0.19679007 -0.15959331
Axis point 0.00000000 224.90663730 229.11626097
Rotation angle (degrees) 140.24985998
Shift along axis -42.65082531
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 28
shifted from previous position = 0.0228
rotated from previous position = 0.0509 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88682818 -0.23410569 -0.39840974 102.63155782
-0.43798841 -0.70069517 -0.56319841 519.75407402
-0.14731582 0.67395906 -0.72393179 250.21245718
Axis 0.96748195 -0.19636048 -0.15944037
Axis point 0.00000000 224.82302925 229.08819200
Rotation angle (degrees) 140.25515764
Shift along axis -42.65894548
Average map value = 0.1109 for 3401 atoms, 1770 outside contour
Average map value = 0.1109 for 3401 atoms, 1770 outside contour
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0277
rotated from previous position = 0.119 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88773516 -0.23286893 -0.39711253 101.94821925
-0.43614356 -0.70150514 -0.56362163 519.65415902
-0.14732651 0.67354481 -0.72431506 250.37946507
Axis 0.96774956 -0.19539029 -0.15900765
Axis point 0.00000000 224.64447067 229.01845950
Rotation angle (degrees) 140.26798555
Shift along axis -42.68728231
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 36
shifted from previous position = 0.0101
rotated from previous position = 0.0384 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88743039 -0.23323831 -0.39757668 102.17484111
-0.43673470 -0.70130263 -0.56341586 519.68061974
-0.14741140 0.67362788 -0.72422052 250.35767544
Axis 0.96766061 -0.19568838 -0.15918228
Axis point 0.00000000 224.69868010 229.04697101
Rotation angle (degrees) 140.26833165
Shift along axis -42.67739283
> ~select #5
Nothing selected
> show #!2 models
> select #2
2 models selected
> view matrix models
> #2,0.19536,0.75362,0.62761,-85.152,-0.79186,-0.25635,0.5543,213.6,0.57862,-0.60527,0.54668,70.661
> view matrix models
> #2,0.11282,0.94881,0.29501,-45.954,-0.85716,-0.057225,0.51186,202.13,0.50254,-0.31062,0.80683,-2.2981
> view matrix models
> #2,0.11282,0.94881,0.29501,-10.942,-0.85716,-0.057225,0.51186,230.24,0.50254,-0.31062,0.80683,26.411
> view matrix models
> #2,-0.3673,0.80202,0.47101,56.376,-0.91933,-0.38991,-0.052965,380.04,0.14117,-0.45246,0.88054,91.186
> view matrix models
> #2,-0.37949,0.87152,0.31056,74.515,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,198.78
> view matrix models
> #2,-0.37949,0.87152,0.31056,77.692,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,195.9
> view matrix models
> #2,-0.4416,0.17153,0.88066,94.799,-0.84825,0.23999,-0.47209,346.93,-0.29232,-0.9555,0.039518,365.71
> view matrix models
> #2,-0.16701,0.27438,0.94701,26.293,-0.9691,-0.22254,-0.10643,372.5,0.18155,-0.93552,0.30307,245.76
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 816, shift = 17.1, angle = 92.5 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884246 0.36253629 0.90084502 32.04958536
-0.12095024 0.90936326 -0.39803210 133.21868643
-0.96349643 -0.20402438 -0.17334571 390.21884814
Axis 0.10022302 0.96310562 -0.24976572
Axis point 169.19260085 0.00000000 200.88498104
Rotation angle (degrees) 104.56110947
Shift along axis 34.05247827
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 40, shift = 0.000646, angle = 0.0027 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884389 0.36253338 0.90084582 32.04982504
-0.12099611 0.90935469 -0.39803771 133.22769414
-0.96349031 -0.20406771 -0.17332869 390.22127920
Axis 0.10020344 0.96310196 -0.24978768
Axis point 169.19590472 0.00000000 200.88843406
Rotation angle (degrees) 104.56090162
Shift along axis 34.05088824
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 40, shift = 2.75e-05, angle = 5.91e-05 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884450 0.36253261 0.90084597 32.05002579
-0.12099600 0.90935500 -0.39803705 133.22750949
-0.96349017 -0.20406771 -0.17332945 390.22138385
Axis 0.10020311 0.96310210 -0.24978726
Axis point 169.19595961 -0.00000000 200.88835343
Rotation angle (degrees) 104.56093288
Shift along axis 34.05087684
> hide #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24143,0.39089,0.88821,30.445,-0.11992,0.89625,-0.42703,139.68,-0.96298,-0.20961,-0.16951,390.31
> view matrix models
> #2,-0.24371,0.41583,0.87618,29.184,-0.11889,0.8838,-0.45252,145.47,-0.96253,-0.21445,-0.16596,390.36
> view matrix models
> #2,-0.23248,0.44368,0.86551,25.173,-0.098419,0.87459,-0.47477,147.23,-0.96761,-0.19556,-0.15966,387.41
> view matrix models
> #2,-0.015904,0.29362,0.95579,-1.8481,0.11672,0.94992,-0.28987,72.596,-0.99304,0.10695,-0.049378,329.9
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3636, correlation about mean = 0.2345, overlap = 5800
steps = 160, shift = 4.43, angle = 14.2 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23589350 0.38613188 0.89177153 30.30521757
0.14116968 0.92155092 -0.36168365 84.35973344
-0.96147045 0.04057228 -0.27189798 372.10342069
Axis 0.21036827 0.96919218 -0.12810818
Axis point 149.90554609 -0.00000000 183.31483684
Rotation angle (degrees) 107.04485499
Shift along axis 40.46655914
> transparency sel 50
> view matrix models
> #2,-0.32117,0.35848,0.87655,50.083,0.35637,0.9033,-0.23885,33.297,-0.87741,0.23567,-0.41786,354.8
> view matrix models
> #2,-0.25849,0.33315,0.90675,38.999,0.20781,0.93585,-0.2846,59.301,-0.9434,0.11486,-0.31114,365.02
> hide #3 models
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> show #3 models
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
B | No description available
C E | No description available
D | No description available
F | No description available
> close #6
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1.pdb" models #3
> relModel #1
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb" models #4
> relModel #1
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb" models #5
> relModel #1
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
B | No description available
C | No description available
> close #6
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
A B | No description available
C E | No description available
D F | No description available
> hide atoms
> show cartoons
> hide #3 models
> hide #5 models
> hide #4 models
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 40
shifted from previous position = 0.0103
rotated from previous position = 0.00699 degrees
atoms outside contour = 6863, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00007640 -0.00005950 0.01644925
0.00007639 0.99999999 -0.00007418 0.00540007
0.00005950 0.00007417 1.00000000 -0.02042262
Axis 0.60809281 -0.48779755 0.62631995
Axis point -36.04322257 258.47150214 0.00000000
Rotation angle (degrees) 0.00698874
Shift along axis -0.00542257
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 12404 atoms
average map value = 0.1322, steps = 204
shifted from previous position = 3.17
rotated from previous position = 16.9 degrees
atoms outside contour = 7037, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.15126719 0.47107682 -0.86902521 263.21094843
0.40313494 0.83210747 0.38089281 -155.24920226
0.90255217 -0.29271785 -0.31577809 100.07490639
Axis -0.35517923 -0.93411153 -0.03582417
Axis point 121.90346818 0.00000000 160.98219047
Rotation angle (degrees) 108.50992410
Shift along axis 47.94790735
> show #3 models
> mmaker #6 to #3
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 D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
> hide #3 models
> ui mousemode right "map eraser"
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J59_004_volume_map_sharp
> (3).mrc"
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
352,352,352, pixel 0.85, shown at level 0.366, step 2, values float32
> close #7
> hide #!2 models
> surface dust #8 size 8.5
> select #8
2 models selected
> close #7
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,35.396,0,1,0,60.903,0,0,1,32.921
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.3457,-0.50036,0.79381,208.17,-0.017535,0.84927,0.52767,14.154,-0.93818,0.1685,-0.30237,329.15
> view matrix models
> #8,-0.51948,-0.14515,0.84206,178.05,0.63577,0.59277,0.49439,-45.989,-0.57091,0.79219,-0.21565,171.93
> view matrix models
> #8,-0.55842,-0.30769,0.77039,216.83,0.59819,0.49406,0.63093,-44.478,-0.57475,0.81316,-0.09184,152.9
> view matrix models
> #8,-0.55842,-0.30769,0.77039,191.12,0.59819,0.49406,0.63093,-46.563,-0.57475,0.81316,-0.09184,158.22
> show #6 models
> ~select #8
Nothing selected
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 168
shifted from previous position = 1.67
rotated from previous position = 11.8 degrees
atoms outside contour = 6854, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 0.00007634 0.00003096 356.91445101
-0.00007636 -0.99999975 -0.00069729 357.06728170
0.00003091 -0.00069729 0.99999976 0.11956672
Axis -0.00001547 0.00034864 -0.99999994
Axis point 178.46403997 178.52684922 0.00000000
Rotation angle (degrees) 179.99562555
Shift along axis -0.00059852
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 40
shifted from previous position = 0.00373
rotated from previous position = 0.0435 degrees
atoms outside contour = 6861, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 0.00004453 0.00006393 356.91507698
-0.00004452 -1.00000000 0.00006135 356.92005524
0.00006393 0.00006135 1.00000000 -0.02104448
Axis -0.00003196 -0.00003068 -1.00000000
Axis point 178.46151168 178.45605515 0.00000000
Rotation angle (degrees) 179.99744898
Shift along axis -0.00131278
> select #8
2 models selected
> view matrix models
> #8,-0.55842,-0.30769,0.77039,144.53,0.59819,0.49406,0.63093,-60.652,-0.57475,0.81316,-0.09184,256.77
> view matrix models
> #8,-0.55842,-0.30769,0.77039,188.5,0.59819,0.49406,0.63093,-43.585,-0.57475,0.81316,-0.09184,207.1
> view matrix models
> #8,0.20416,-0.32979,0.92171,53.292,0.8306,0.55667,0.015197,-5.7187,-0.5181,0.76247,0.38758,141.12
> view matrix models
> #8,-0.17775,-0.55408,0.81327,158.88,0.42359,0.70287,0.57144,-38.275,-0.88824,0.44606,0.10977,280.75
> view matrix models
> #8,-0.44365,-0.53212,0.72113,209.28,0.54415,0.47941,0.68853,-40.877,-0.71209,0.69787,0.076868,222.08
> view matrix models
> #8,-0.44365,-0.53212,0.72113,201.21,0.54415,0.47941,0.68853,-58.258,-0.71209,0.69787,0.076868,191.6
> view matrix models
> #8,-0.44365,-0.53212,0.72113,198.44,0.54415,0.47941,0.68853,-54.781,-0.71209,0.69787,0.076868,186.46
> view matrix models
> #8,-0.078986,-0.30105,0.95033,78.334,0.99624,-0.057911,0.064456,35.555,0.03563,0.95185,0.30449,4.0251
> view matrix models
> #8,-0.078986,-0.30105,0.95033,83.821,0.99624,-0.057911,0.064456,34.166,0.03563,0.95185,0.30449,22.679
> view matrix models
> #8,-0.13528,-0.37298,0.91792,107.12,0.9291,0.27408,0.24829,-27.377,-0.34419,0.88644,0.30946,90.098
> view matrix models
> #8,-0.13528,-0.37298,0.91792,107.41,0.9291,0.27408,0.24829,-25.4,-0.34419,0.88644,0.30946,74.434
> view matrix models
> #8,0.021026,-0.64563,0.76336,142.78,0.95068,0.24925,0.18463,-16.653,-0.30947,0.72183,0.61903,50.881
> view matrix models
> #8,0.18242,-0.5728,0.79914,102.63,0.95907,0.28269,-0.016302,4.2907,-0.21658,0.76941,0.60092,32.168
> view matrix models
> #8,0.18242,-0.5728,0.79914,103.51,0.95907,0.28269,-0.016302,-14.792,-0.21658,0.76941,0.60092,29.021
> view matrix models
> #8,0.18242,-0.5728,0.79914,103.75,0.95907,0.28269,-0.016302,-13.773,-0.21658,0.76941,0.60092,25.236
> view matrix models
> #8,0.19689,-0.59123,0.7821,106.42,0.95308,0.30251,-0.011255,-16.342,-0.22993,0.74762,0.62305,27.429
> view matrix models
> #8,0.16349,-0.53138,0.83121,96.478,0.91695,0.39269,0.070685,-34.591,-0.36397,0.75062,0.55145,57.366
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2099, correlation about mean = -0.0466, overlap = 1148
steps = 220, shift = 8.88, angle = 20.7 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.16970377 -0.22411591 0.95967322 38.04053966
0.82808228 0.56039048 -0.01556391 -26.95927500
-0.53430362 0.79732965 0.28068680 115.40605181
Axis 0.40645268 0.74699927 0.52610674
Axis point 84.17805896 0.00000000 56.92499809
Rotation angle (degrees) 89.69114416
Shift along axis 56.03902271
> hide #!8 models
> hide #7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #8,0.17985,-0.20944,0.96114,34.185,0.82577,0.56311,-0.031812,-24.805,-0.53457,0.7994,0.27422,116.02
> view matrix models
> #8,-0.19365,-0.33381,0.92253,114.87,-0.70512,-0.60645,-0.36745,423.6,0.68213,-0.72166,-0.11794,196.81
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 196, shift = 4.16, angle = 13 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07683115 -0.17561277 0.98145662 66.44166832
-0.66408769 -0.72522667 -0.18175198 411.16957530
0.74369650 -0.66573749 -0.06090228 170.05104945
Axis -0.66519466 0.32677996 -0.67136497
Axis point 7.75299271 239.88960504 0.00000000
Rotation angle (degrees) 158.66671698
Shift along axis -24.00098327
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 44, shift = 0.00106, angle = 0.00247 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07685176 -0.17562808 0.98145227 66.44848746
-0.66411122 -0.72519937 -0.18177500 411.17240045
0.74367337 -0.66576320 -0.06090373 170.05786271
Axis -0.66518608 0.32679973 -0.67136385
Axis point 7.75566835 239.89404572 0.00000000
Rotation angle (degrees) 158.66630362
Shift along axis -24.00027887
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 44, shift = 0.00214, angle = 0.00428 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07680221 -0.17565442 0.98145143 66.44396733
-0.66407552 -0.72523465 -0.18176462 411.17025225
0.74371036 -0.66571781 -0.06094818 170.05404481
Axis -0.66520863 0.32678246 -0.67134991
Axis point 7.74491366 239.89221167 -0.00000000
Rotation angle (degrees) 158.66868085
Shift along axis -24.00164195
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select down
2 models selected
> volume flip #8
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip as #9, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> hide #!9 models
> show #!9 models
> select #9
2 models selected
> view matrix models
> #9,0.04932,0.5784,-0.81426,225.85,0.77832,-0.53317,-0.33159,193.54,-0.62593,-0.6174,-0.47647,432.54
> view matrix models
> #9,0.49864,0.44515,-0.74377,167.72,0.18866,-0.89322,-0.40812,346.38,-0.84603,0.063187,-0.52938,372.95
> view matrix models
> #9,0.41566,0.19473,-0.88843,240.37,-0.83603,-0.30285,-0.45753,418.6,-0.35815,0.93293,0.036921,80.781
> view matrix models
> #9,0.18699,-0.28999,-0.93858,354,0.30934,-0.88945,0.33644,207.89,-0.93239,-0.35325,-0.076615,374.31
> view matrix models
> #9,0.12166,-0.27135,-0.95476,363.51,0.35041,-0.88823,0.29709,207.97,-0.92866,-0.37071,-0.01298,366.08
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.12166,-0.27135,-0.95476,343.55,0.35041,-0.88823,0.29709,204.63,-0.92866,-0.37071,-0.01298,384.14
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03988, overlap = 1580
steps = 48, shift = 0.0161, angle = 0.00778 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07667600 -0.17562499 0.98146657 66.40220937
-0.66405605 -0.72527845 -0.18166098 411.15872420
0.74374077 -0.66567786 -0.06101339 170.05477366
Axis -0.66525588 0.32674168 -0.67132294
Axis point 7.71835621 239.88762888 0.00000000
Rotation angle (degrees) 158.66732589
Shift along axis -23.99344049
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 84, shift = 0.0157, angle = 0.009 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07682622 -0.17562423 0.98145496 66.44206918
-0.66408132 -0.72523107 -0.18175771 411.17012882
0.74370270 -0.66572968 -0.06091201 170.05004664
Axis -0.66519758 0.32677973 -0.67136219
Axis point 7.75121505 239.88987802 0.00000000
Rotation angle (degrees) 158.66744100
Shift along axis -24.00021217
> view matrix models
> #9,0.12166,-0.27135,-0.95476,338.02,0.35041,-0.88823,0.29709,203.08,-0.92866,-0.37071,-0.01298,379.52
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.30016,-0.86169,-0.40914,310.95,-0.62921,-0.50123,0.59402,242.86,-0.71693,0.079138,-0.69264,391.26
> view matrix models
> #9,0.079463,-0.47579,-0.87596,361.79,-0.033015,-0.87952,0.47472,229.87,-0.99629,-0.0088031,-0.085597,347.7
> view matrix models
> #9,0.41919,-0.72698,-0.54387,295.14,-0.54116,-0.68106,0.49326,272.69,-0.729,0.087548,-0.6789,389.59
> view matrix models
> #9,-0.24911,-0.67335,-0.6961,410.62,-0.72999,-0.34178,0.59185,234.54,-0.63644,0.65558,-0.4064,247.91
> view matrix models
> #9,0.38176,-0.48586,-0.78626,304.1,-0.52937,-0.81227,0.24491,330.41,-0.75764,0.32273,-0.56729,341.04
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 40, shift = 0.000846, angle = 0.00177 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07680654 -0.17560484 0.98145997 66.43537485
-0.66409320 -0.72522729 -0.18172939 411.16781129
0.74369413 -0.66573891 -0.06091578 170.05270073
Axis -0.66520310 0.32677576 -0.67135865
Axis point 7.74972828 239.88942606 0.00000000
Rotation angle (degrees) 158.66589087
Shift along axis -23.99969612
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 40, shift = 0.00125, angle = 0.00125 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07681767 -0.17562278 0.98145589 66.43984164
-0.66408848 -0.72522635 -0.18175040 411.16938528
0.74369719 -0.66573520 -0.06091887 170.05309874
Axis -0.66520021 0.32678120 -0.67135886
Axis point 7.74944501 239.89073787 0.00000000
Rotation angle (degrees) 158.66693629
Shift along axis -24.00002709
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 435032 points
correlation = 0.2522, correlation about mean = -0.0372, overlap = 1.179e+04
steps = 324, shift = 5.58, angle = 29.2 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip (#9)
relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.07209466 -0.25700523 -0.96371709 344.01508219
-0.25749943 -0.93827144 0.23095609 315.15876008
-0.96358516 0.23150590 -0.13382306 321.33072132
Axis 0.73215596 -0.17567940 -0.65809148
Axis point 0.00000000 198.81231893 315.31278484
Rotation angle (degrees) 179.97848683
Shift along axis -14.95921604
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!8 models
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!2 models
> ~select #9
Nothing selected
> show #7 models
> hide #6 models
> hide #!1 models
> select #7
1 model selected
> view matrix models
> #7,0.28314,0.80804,0.51663,178.11,-0.89657,0.0317,0.44178,178.55,0.34059,-0.58828,0.73343,173.27
> view matrix models
> #7,-0.85167,0.44193,-0.28171,178.2,0.13709,-0.33096,-0.93363,178.47,-0.50584,-0.83376,0.22128,173.34
> view matrix models
> #7,-0.052894,0.17656,-0.98287,178.14,0.95344,0.30156,0.0028629,178.4,0.2969,-0.93695,-0.18429,173.28
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.052894,0.17656,-0.98287,123.75,0.95344,0.30156,0.0028629,168.98,0.2969,-0.93695,-0.18429,135.65
> view matrix models
> #7,-0.052894,0.17656,-0.98287,171.65,0.95344,0.30156,0.0028629,239.46,0.2969,-0.93695,-0.18429,240.81
> view matrix models
> #7,-0.052894,0.17656,-0.98287,168.29,0.95344,0.30156,0.0028629,214.9,0.2969,-0.93695,-0.18429,234.8
> transparency #2.1 0
> volume erase #2 center 168.29,214.9,234.8 radius 57.895
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> view matrix models
> #7,-0.052894,0.17656,-0.98287,158.31,0.95344,0.30156,0.0028629,232.11,0.2969,-0.93695,-0.18429,231.78
> volume erase #10 center 158.31,232.11,231.78 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,179.95,0.95344,0.30156,0.0028629,219.57,0.2969,-0.93695,-0.18429,237.28
> view matrix models
> #7,-0.052894,0.17656,-0.98287,196.31,0.95344,0.30156,0.0028629,220.25,0.2969,-0.93695,-0.18429,246.32
> volume erase #10 center 196.31,220.25,246.32 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,185.48,0.95344,0.30156,0.0028629,234.46,0.2969,-0.93695,-0.18429,244.14
> view matrix models
> #7,-0.052894,0.17656,-0.98287,151.71,0.95344,0.30156,0.0028629,160.15,0.2969,-0.93695,-0.18429,262.05
> view matrix models
> #7,-0.052894,0.17656,-0.98287,147.93,0.95344,0.30156,0.0028629,158.34,0.2969,-0.93695,-0.18429,267.59
> view matrix models
> #7,-0.052894,0.17656,-0.98287,139.18,0.95344,0.30156,0.0028629,153.5,0.2969,-0.93695,-0.18429,267
> volume erase #10 center 139.18,153.5,267 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,140,0.95344,0.30156,0.0028629,152.53,0.2969,-0.93695,-0.18429,263.01
> view matrix models
> #7,-0.052894,0.17656,-0.98287,156.67,0.95344,0.30156,0.0028629,178.21,0.2969,-0.93695,-0.18429,266.42
> volume erase #10 center 156.67,178.21,266.42 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,158.47,0.95344,0.30156,0.0028629,179.86,0.2969,-0.93695,-0.18429,260.63
> view matrix models
> #7,-0.052894,0.17656,-0.98287,146.27,0.95344,0.30156,0.0028629,179.75,0.2969,-0.93695,-0.18429,264.96
> view matrix models
> #7,-0.052894,0.17656,-0.98287,136.73,0.95344,0.30156,0.0028629,165.7,0.2969,-0.93695,-0.18429,256.45
> volume erase #10 center 136.73,165.7,256.45 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,170.65,0.95344,0.30156,0.0028629,257.57,0.2969,-0.93695,-0.18429,281.54
> view matrix models
> #7,-0.052894,0.17656,-0.98287,198.12,0.95344,0.30156,0.0028629,237.97,0.2969,-0.93695,-0.18429,234.34
> volume erase #10 center 198.12,237.97,234.34 radius 57.895
> close #7
> show #!1 models
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points
correlation = 0.4197, correlation about mean = 0.1732, overlap = 5606
steps = 100, shift = 2.13, angle = 5.64 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.26232817 0.42310640 0.86727444 32.84932501
0.23389320 0.89982892 -0.36824168 75.35914970
-0.93620401 0.10624943 -0.33501218 371.04180450
Axis 0.25313923 0.96214902 -0.10094453
Axis point 142.07695422 0.00000000 181.57625532
Rotation angle (degrees) 110.41122784
Shift along axis 43.36754334
> select #10
2 models selected
> view matrix models
> #10,-0.26233,0.42311,0.86727,32.251,0.23389,0.89983,-0.36824,72.484,-0.9362,0.10625,-0.33501,370.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.13878,0.40417,0.9041,8.8226,0.22067,0.9026,-0.36963,74.459,-0.96543,0.14821,-0.21445,349.11
> view matrix models
> #10,0.081829,0.24713,0.96552,-14.455,0.27881,0.92441,-0.26024,43.68,-0.95685,0.29049,0.0067426,290.35
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points
correlation = 0.4197, correlation about mean = 0.1733, overlap = 5606
steps = 228, shift = 2.88, angle = 23.2 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.26246485 0.42303734 0.86726677 32.87464761
0.23392580 0.89986112 -0.36814227 75.32527217
-0.93615756 0.10625167 -0.33514125 371.06459232
Axis 0.25309913 0.96216476 -0.10089498
Axis point 142.08264269 0.00000000 181.57434136
Rotation angle (degrees) 110.41836671
Shift along axis 43.35731307
> show #6 models
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> hide #!10 models
> show #!8 models
> hide #!1 models
> ~select #10
Nothing selected
> hide #6 models
> select #7
1 model selected
> view matrix models
> #7,0.92464,0.25458,-0.28325,178.06,0.04684,0.66208,0.74796,178.47,0.37795,-0.70486,0.60026,173.27
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.92464,0.25458,-0.28325,204.47,0.04684,0.66208,0.74796,168.78,0.37795,-0.70486,0.60026,117.92
> view matrix models
> #7,0.92464,0.25458,-0.28325,205.35,0.04684,0.66208,0.74796,172.6,0.37795,-0.70486,0.60026,132.71
> view matrix models
> #7,0.92464,0.25458,-0.28325,202.38,0.04684,0.66208,0.74796,170.72,0.37795,-0.70486,0.60026,135.25
> view matrix models
> #7,0.92464,0.25458,-0.28325,208.14,0.04684,0.66208,0.74796,169.1,0.37795,-0.70486,0.60026,122.9
> volume #8 level 0.8304
> view matrix models
> #7,0.92464,0.25458,-0.28325,209.46,0.04684,0.66208,0.74796,167.64,0.37795,-0.70486,0.60026,121.48
> volume erase #8 center 209.46,167.64,121.48 radius 64.178
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> view matrix models
> #7,0.92464,0.25458,-0.28325,202.68,0.04684,0.66208,0.74796,128.68,0.37795,-0.70486,0.60026,117.72
> volume erase #11 center 202.68,128.68,117.72 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,183.78,0.04684,0.66208,0.74796,136.58,0.37795,-0.70486,0.60026,112.38
> volume erase #11 center 183.78,136.58,112.38 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,262.78,0.04684,0.66208,0.74796,132.37,0.37795,-0.70486,0.60026,184.94
> view matrix models
> #7,0.92464,0.25458,-0.28325,269.47,0.04684,0.66208,0.74796,136.95,0.37795,-0.70486,0.60026,179.85
> view matrix models
> #7,0.92464,0.25458,-0.28325,267.59,0.04684,0.66208,0.74796,127.26,0.37795,-0.70486,0.60026,154.16
> view matrix models
> #7,0.92464,0.25458,-0.28325,261.44,0.04684,0.66208,0.74796,136.21,0.37795,-0.70486,0.60026,158.39
> volume erase #11 center 261.44,136.21,158.39 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,234.76,0.04684,0.66208,0.74796,204.63,0.37795,-0.70486,0.60026,115.7
> view matrix models
> #7,0.92464,0.25458,-0.28325,232.48,0.04684,0.66208,0.74796,207.24,0.37795,-0.70486,0.60026,119.09
> volume erase #11 center 232.48,207.24,119.09 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,211.86,0.04684,0.66208,0.74796,185.05,0.37795,-0.70486,0.60026,105.87
> view matrix models
> #7,0.92464,0.25458,-0.28325,195.04,0.04684,0.66208,0.74796,187.39,0.37795,-0.70486,0.60026,114.92
> view matrix models
> #7,0.92464,0.25458,-0.28325,201.04,0.04684,0.66208,0.74796,190.35,0.37795,-0.70486,0.60026,113.3
> volume erase #11 center 201.04,190.35,113.3 radius 64.178
> show #!1 models
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3648, correlation about mean = -0.1049, overlap = 2621
steps = 72, shift = 2.57, angle = 2.92 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05111081 -0.21510165 0.97525327 67.52834138
-0.64952035 -0.73462917 -0.19606954 411.11615250
0.75862440 -0.64346813 -0.10216541 168.35220279
Axis -0.67771084 0.32814528 -0.65804915
Axis point 0.00000000 241.21252430 -1.00026216
Rotation angle (degrees) 160.72632370
Shift along axis -21.64288928
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621
steps = 40, shift = 0.0141, angle = 0.00956 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05107225 -0.21496635 0.97528512 67.48907810
-0.64946346 -0.73471119 -0.19595064 411.10839498
0.75867570 -0.64341970 -0.10208944 168.33302170
Axis -0.67772214 0.32806961 -0.65807524
Axis point 0.00000000 241.19521972 -0.99729201
Rotation angle (degrees) 160.72350203
Shift along axis -21.64246440
Correlation = 0.3649, Correlation about mean = -0.1049, Overlap = 2621
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621
steps = 28, shift = 0.011, angle = 0.00422 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05110002 -0.21502631 0.97527045 67.51163904
-0.64943800 -0.73471600 -0.19601698 411.10850225
0.75869563 -0.64339417 -0.10210226 168.32377829
Axis -0.67771626 0.32808172 -0.65807526
Axis point 0.00000000 241.19615320 -1.00289431
Rotation angle (degrees) 160.72744238
Shift along axis -21.64626553
> close #7
> volume #8 level 0.4211
> hide #!8 models
> volume #11 level 0.6377
> volume #11 level 0.4713
> show #!10 models
> hide #!10 models
> show #!10 models
> select #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.14971,0.63965,-0.75394,191.13,-0.95888,-0.2799,-0.047058,377.99,-0.24113,0.71589,0.65525,40.47
> view matrix models
> #11,-0.069022,0.30969,-0.94833,249.55,0.96027,0.27828,0.020987,-16.584,0.2704,-0.9092,-0.3166,311.78
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.069022,0.30969,-0.94833,292.24,0.96027,0.27828,0.020987,-16.748,0.2704,-0.9092,-0.3166,306.11
> view matrix models
> #11,-0.069022,0.30969,-0.94833,288.83,0.96027,0.27828,0.020987,-15.141,0.2704,-0.9092,-0.3166,305.54
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.12042,0.37081,-0.92087,284.98,0.89214,0.44729,0.063446,-33.276,0.43542,-0.8139,-0.38467,274.73
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points
correlation = 0.3705, correlation about mean = -0.01342, overlap = 9885
steps = 84, shift = 3.3, angle = 7.24 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.08967779 0.29999028 -0.94971770 295.49237204
0.84493489 0.52775912 0.08692132 -41.96570345
0.52729773 -0.79465472 -0.30080053 248.18221209
Axis -0.48858097 -0.81858128 0.30201543
Axis point 60.64458577 -0.00000000 223.51625228
Rotation angle (degrees) 115.55387500
Shift along axis -35.06475327
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points
correlation = 0.3706, correlation about mean = -0.01331, overlap = 9885
steps = 40, shift = 0.0143, angle = 0.0103 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.08981970 0.29998685 -0.94970537 295.52003565
0.84486634 0.52788229 0.08683967 -41.94876855
0.52738342 -0.79457419 -0.30086302 248.17026594
Axis -0.48850161 -0.81863956 0.30198584
Axis point 60.66605513 0.00000000 223.51111811
Rotation angle (degrees) 115.55645450
Shift along axis -35.07718649
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> close #9
> show #!2 models
> hide #!11 models
> ~select #11
Nothing selected
> show #6 models
> hide #!2 models
> show #!2 models
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 434908 points
correlation = 0.8681, correlation about mean = 0.7943, overlap = 2.493e+04
steps = 100, shift = 2.6, angle = 5.47 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.99999417 -0.00078818 -0.00332112 0.86833791
0.00079720 0.99999599 0.00271726 -0.70720618
0.00331897 -0.00271989 0.99999079 0.00769659
Axis -0.62300052 -0.76083593 0.18165636
Axis point -1.67706066 0.00000000 261.17922578
Rotation angle (degrees) 0.25002110
Shift along axis -0.00150896
> hide #!1 models
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms
average map value = 0.1247, steps = 124
shifted from previous position = 2.69
rotated from previous position = 12.5 degrees
atoms outside contour = 7351, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.25275147 -0.43670415 -0.86336907 353.51447381
-0.44938591 -0.84323715 0.29496333 308.88812835
-0.85683660 0.31343349 -0.40937812 323.84932290
Axis 0.79143097 -0.27991074 -0.54340316
Axis point 0.00000000 215.73050893 284.44415750
Rotation angle (degrees) 179.33140963
Shift along axis 17.34045325
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms
average map value = 0.1247, steps = 36
shifted from previous position = 0.00249
rotated from previous position = 0.00661 degrees
atoms outside contour = 7351, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.25279114 -0.43660663 -0.86340677 353.49888697
-0.44933375 -0.84329450 0.29487884 308.90364784
-0.85685225 0.31341505 -0.40935948 323.85331097
Axis 0.79144345 -0.27985911 -0.54341158
Axis point 0.00000000 215.71863017 284.44492018
Rotation angle (degrees) 179.32902903
Shift along axis 17.33923677
> transparency #2.1#10.1 50
> hide #!2 models
> show #!8 models
> select #8
2 models selected
> view matrix models
> #8,0.33902,0.03981,-0.93994,229.8,-0.92382,-0.17477,-0.34061,394.45,-0.17784,0.9838,-0.022475,72.918
> view matrix models
> #8,-0.19081,0.15972,-0.96855,298.63,-0.9771,-0.1256,0.17178,326.79,-0.094217,0.97914,0.18003,33.4
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.19081,0.15972,-0.96855,333.9,-0.9771,-0.1256,0.17178,339.76,-0.094217,0.97914,0.18003,31.589
> view matrix models
> #8,-0.19081,0.15972,-0.96855,336.31,-0.9771,-0.1256,0.17178,330.87,-0.094217,0.97914,0.18003,34.463
> view matrix models
> #8,-0.19081,0.15972,-0.96855,332.19,-0.9771,-0.1256,0.17178,338.81,-0.094217,0.97914,0.18003,28.17
> view matrix models
> #8,-0.19081,0.15972,-0.96855,344.81,-0.9771,-0.1256,0.17178,333.8,-0.094217,0.97914,0.18003,27.752
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.39538,0.22669,-0.8901,233.97,0.79273,0.40527,0.45534,-53.893,0.46395,-0.88565,-0.019473,233.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.39538,0.22669,-0.8901,225.01,0.79273,0.40527,0.45534,-60.792,0.46395,-0.88565,-0.019473,244.4
> view matrix models
> #8,0.39538,0.22669,-0.8901,226.27,0.79273,0.40527,0.45534,-67.659,0.46395,-0.88565,-0.019473,244.84
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 47154 points
correlation = 0.3601, correlation about mean = -0.01926, overlap = 2801
steps = 244, shift = 6.57, angle = 20.9 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.50275518 0.77664634 0.37954926 71.44698114
0.77480667 0.59955666 -0.20051529 -35.12156246
-0.38329076 0.19326720 -0.90318100 318.59922133
Axis 0.45869577 0.88859079 -0.00214294
Axis point 85.22138435 0.00000000 150.24137730
Rotation angle (degrees) 154.58056842
Shift along axis 0.88099311
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
——— End of log from Tue Feb 22 21:05:12 2022 ———
opened ChimeraX session
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!1 models
> show #!2 models
> close #11
> close #8
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/2n5e.pdb"
2n5e.pdb title:
The 3D solution structure of discoidal high-density lipoprotein particles
[more info...]
Chain information for 2n5e.pdb
---
Chain | Description
7.1/A 7.2/A 7.3/A 7.4/A 7.5/A 7.6/A 7.7/A 7.8/A 7.9/A 7.10/A 7.1/B 7.2/B 7.3/B
7.4/B 7.5/B 7.6/B 7.7/B 7.8/B 7.9/B 7.10/B | apolipoprotein A-I
> close #7.2-10
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> hide #!2 models
> hide #!1 models
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 352
shifted from previous position = 4.55
rotated from previous position = 50.7 degrees
atoms outside contour = 2605, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51892205 0.80965860 -0.27417668 164.22917225
-0.84272074 -0.43077092 0.32289035 300.54198392
0.14332362 0.39860929 0.90585262 -107.70830576
Axis 0.04438420 -0.24472630 -0.96857580
Axis point 169.29706156 116.85077370 0.00000000
Rotation angle (degrees) 121.46114137
Shift along axis 38.06231174
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 40
shifted from previous position = 0.00569
rotated from previous position = 0.00161 degrees
atoms outside contour = 2609, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51894067 0.80965192 -0.27416117 164.23500046
-0.84270669 -0.43078495 0.32290828 300.54258112
0.14333881 0.39860769 0.90585092 -107.71085737
Axis 0.04437330 -0.24472913 -0.96857558
Axis point 169.29862447 116.85084764 0.00000000
Rotation angle (degrees) 121.46229524
Shift along axis 38.06223078
> show #4 models
> hide #!7 models
> hide #6 models
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 184
shifted from previous position = 2.68
rotated from previous position = 43.1 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23696585 -0.97040692 -0.04644960 286.31819473
0.13996862 0.08141367 -0.98680321 234.14224375
0.96138231 0.22733718 0.15511878 -33.92541253
Axis 0.62926604 -0.52234025 0.57548668
Axis point 0.00000000 269.88096267 6.34604794
Rotation angle (degrees) 105.26304401
Shift along axis 38.34477607
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.0184 degrees
atoms outside contour = 1053, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23699244 -0.97040417 -0.04637137 286.30251238
0.14028426 0.08141314 -0.98675843 234.09383454
0.96132975 0.22734912 0.15542673 -33.96007421
Axis 0.62921931 -0.52224780 0.57562166
Axis point 0.00000000 269.87054516 6.30278577
Rotation angle (degrees) 105.25312557
Shift along axis 38.34392482
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 44
shifted from previous position = 0.0177
rotated from previous position = 0.024 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23699037 -0.97040260 -0.04641486 286.30808679
0.13987427 0.08136006 -0.98682101 234.17141287
0.96139000 0.22737483 0.15501591 -33.91830894
Axis 0.62930653 -0.52233598 0.57544628
Axis point 0.00000000 269.87165306 6.36745226
Rotation angle (degrees) 105.26696289
Shift along axis 38.34122922
> show #3 models
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 44
shifted from previous position = 0.0174
rotated from previous position = 0.02 degrees
atoms outside contour = 1053, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23696878 -0.97040926 -0.04638578 286.31082660
0.14021616 0.08140780 -0.98676855 234.10798884
0.96134552 0.22732931 0.15535816 -33.95179699
Axis 0.62922296 -0.52227064 0.57559694
Axis point 0.00000000 269.87770153 6.30937551
Rotation angle (degrees) 105.25602295
Shift along axis 38.34306534
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.0232 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23695180 -0.97040946 -0.04646826 286.32373425
0.13981736 0.08139458 -0.98682623 234.17404048
0.96140779 0.22733318 0.15496668 -33.91113966
Axis 0.62929239 -0.52237681 0.57542468
Axis point 0.00000000 269.88626156 6.36736238
Rotation angle (degrees) 105.26854490
Shift along axis 38.34095150
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 40
shifted from previous position = 0.00386
rotated from previous position = 0.0076 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23701158 -0.97039892 -0.04638334 286.30019564
0.13991374 0.08134082 -0.98681700 234.16833276
0.96137903 0.22739739 0.15505086 -33.92599735
Axis 0.62931286 -0.52231123 0.57546182
Axis point 0.00000000 269.86512738 6.36383820
Rotation angle (degrees) 105.26586629
Shift along axis 38.34052770
> show #!2 models
> show #6 models
> hide #!2 models
> hide #!10 models
> hide #6 models
> show #6 models
> mmaker #6 to #3
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 D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!2 models
> show #!1 models
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.4911, correlation about mean = 0.2779, overlap = 6002
steps = 1308, shift = 0.661, angle = 22 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27793747 -0.14035072 -0.95029069 409.92559615
0.39452131 0.88530641 -0.24614115 -49.02432671
0.87584454 -0.44332178 -0.19068848 109.24693947
Axis -0.10307165 -0.95457032 0.27959209
Axis point 169.03926821 0.00000000 207.85299225
Rotation angle (degrees) 106.95735055
Shift along axis 35.09003774
> show #!10 models
> hide #!2 models
> hide #!1 models
> show #!2 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 44
shifted from previous position = 0.00219
rotated from previous position = 0.0172 degrees
atoms outside contour = 2607, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51889139 0.80974271 -0.27398626 164.17754795
-0.84268736 -0.43067692 0.32310277 300.48501792
0.14363056 0.39854000 0.90583449 -107.74724207
Axis 0.04421738 -0.24478525 -0.96856853
Axis point 169.27126594 116.83993981 0.00000000
Rotation angle (degrees) 121.45756347
Shift along axis 38.06578928
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 44
shifted from previous position = 0.00282
rotated from previous position = 0.00397 degrees
atoms outside contour = 2606, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51894411 0.80971407 -0.27397106 164.19040191
-0.84265984 -0.43073928 0.32309143 300.49449446
0.14360158 0.39853079 0.90584314 -107.74009884
Axis 0.04422032 -0.24476870 -0.96857258
Axis point 169.27313448 116.84271119 0.00000000
Rotation angle (degrees) 121.46113819
Shift along axis 38.06301215
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.14665,-0.10019,0.9841,42.803,-0.93066,-0.32317,-0.17158,431.35,0.33522,-0.94102,-0.045847,294.18
> view matrix models
> #3,-0.24212,-0.16715,0.95574,75.904,-0.91312,-0.29375,-0.2827,443.12,0.328,-0.94116,-0.081503,301.82
> view matrix models
> #3,-0.22781,0.0025001,0.9737,41.665,-0.95433,-0.19906,-0.22277,423.77,0.19327,-0.97998,0.047735,309.02
> view matrix models
> #3,-0.31679,-0.24249,0.91698,108.61,-0.87534,-0.29756,-0.38109,454.64,0.36527,-0.92339,-0.118,298.78
> view matrix models
> #3,-0.20831,0.16138,0.96466,13.134,-0.97765,-0.063166,-0.20055,401.06,0.028569,-0.98487,0.17093,316.86
> view matrix models
> #3,-0.18189,0.029376,0.98288,27.434,-0.97841,0.094327,-0.18388,371.75,-0.098114,-0.99511,0.011585,369.25
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.18189,0.029376,0.98288,26.801,-0.97841,0.094327,-0.18388,370.7,-0.098114,-0.99511,0.011585,365.44
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 220
shifted from previous position = 5.16
rotated from previous position = 26.4 degrees
atoms outside contour = 2605, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51865164 0.80982057 -0.27420999 164.16314366
-0.84285174 -0.43044060 0.32298891 300.49787860
0.14353196 0.39863709 0.90580740 -107.73453379
Axis 0.04433389 -0.24481919 -0.96855463
Axis point 169.29026360 116.83700867 0.00000000
Rotation angle (degrees) 121.44248630
Shift along axis 38.05712471
> hide #!2 models
> view matrix models
> #3,-0.095949,-0.048917,0.99418,23.903,-0.93262,-0.34465,-0.10697,422.69,0.34788,-0.93745,-0.012552,284.37
> view matrix models
> #3,-0.095949,-0.048917,0.99418,24.499,-0.93262,-0.34465,-0.10697,420.51,0.34788,-0.93745,-0.012552,282.55
> ui mousemode right "map eraser"
> volume erase #10 center 197.01,182.51,231.59 radius 31.633
> volume erase #10 center 213.27,171.82,231.83 radius 31.633
> volume erase #10 center 199.27,226.74,192.59 radius 31.633
> volume erase #10 center 201.83,210.63,213.73 radius 31.633
> close #8
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 84
shifted from previous position = 4.01
rotated from previous position = 2.96 degrees
atoms outside contour = 2586, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47450864 0.83236882 -0.28636287 154.63058051
-0.86693279 -0.38553270 0.31589884 297.74905925
0.15254210 0.39815408 0.90454642 -108.87748698
Axis 0.04681588 -0.24980441 -0.96716391
Axis point 169.11832797 115.96117517 0.00000000
Rotation angle (degrees) 118.53838807
Shift along axis 38.16251411
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 48
shifted from previous position = 0.00277
rotated from previous position = 0.00477 degrees
atoms outside contour = 2584, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47448892 0.83239630 -0.28631566 154.61369255
-0.86692974 -0.38549828 0.31594921 297.73456104
0.15262076 0.39812996 0.90454377 -108.88430164
Axis 0.04677274 -0.24981834 -0.96716240
Axis point 169.11102884 115.95863363 0.00000000
Rotation angle (degrees) 118.53670909
Shift along axis 38.16095498
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 60
shifted from previous position = 0.0162
rotated from previous position = 0.0207 degrees
atoms outside contour = 2591, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47456944 0.83227118 -0.28654585 154.70120447
-0.86694397 -0.38562941 0.31575007 297.80757285
0.15228918 0.39826452 0.90454042 -108.84769154
Axis 0.04696579 -0.24977725 -0.96716366
Axis point 169.15292707 115.96995015 0.00000000
Rotation angle (degrees) 118.54372018
Shift along axis 38.15363917
> show #!2 models
> show #!7 models
> show #7.1 models
> select #7.1
5464 atoms, 5510 bonds, 334 residues, 1 model selected
> close #8
> close #8
> ui mousemode right "translate selected models"
> view matrix models #7.1,1,0,0,169.78,0,1,0,228.66,0,0,1,242.62
> view matrix models #7.1,1,0,0,141.19,0,1,0,179.49,0,0,1,253.16
> view matrix models #7.1,1,0,0,139.34,0,1,0,181.33,0,0,1,279.32
> view matrix models #7.1,1,0,0,140.66,0,1,0,199.74,0,0,1,261.78
> view matrix models #7.1,1,0,0,152.52,0,1,0,194.28,0,0,1,257.24
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.96441,0.048869,0.25985,165.75,0.098602,0.8454,-0.52495,167.67,-0.24533,0.53189,0.8105,246.45
> view matrix models
> #7.1,0.52404,0.070357,0.84878,205.22,0.25659,0.93724,-0.23611,177.31,-0.81212,0.34152,0.4731,245.12
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.96,0.25659,0.93724,-0.23611,166.4,-0.81212,0.34152,0.4731,253.15
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.06,0.25659,0.93724,-0.23611,172.5,-0.81212,0.34152,0.4731,255.75
> view matrix models
> #7.1,0.52404,0.070357,0.84878,220.15,0.25659,0.93724,-0.23611,172.23,-0.81212,0.34152,0.4731,250.53
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.93,0.25659,0.93724,-0.23611,169.22,-0.81212,0.34152,0.4731,253.47
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.24,0.25659,0.93724,-0.23611,170.23,-0.81212,0.34152,0.4731,253.64
> view matrix models
> #7.1,0.52404,0.070357,0.84878,216.82,0.25659,0.93724,-0.23611,165.96,-0.81212,0.34152,0.4731,248.26
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.73952,-0.17388,0.65029,205.07,0.14405,0.98456,0.099452,184.79,-0.65754,0.020126,0.75315,262.95
> view matrix models
> #7.1,0.73125,-0.084624,0.67684,205.42,0.062378,0.99641,0.057187,184.4,-0.67925,0.00040129,0.73391,262.74
> view matrix models
> #7.1,0.69799,-0.10334,0.70861,208.03,0.074484,0.99464,0.071682,184.87,-0.71222,0.0027467,0.70195,261.87
> view matrix models
> #7.1,0.63726,0.053079,0.76882,210.42,0.18684,0.95722,-0.22096,168.07,-0.74766,0.28445,0.60008,253.89
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,0.63726,0.053079,0.76882,208.69,0.18684,0.95722,-0.22096,171.97,-0.74766,0.28445,0.60008,254.92
> view matrix models
> #7.1,0.63726,0.053079,0.76882,209.09,0.18684,0.95722,-0.22096,174.45,-0.74766,0.28445,0.60008,259.11
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.62362,0.070465,0.77855,209.66,0.22628,0.93702,-0.26606,171.53,-0.74826,0.34209,0.5684,256.78
> view matrix models
> #7.1,0.61203,0.086506,0.78609,210.1,0.26096,0.91623,-0.30401,169.1,-0.74654,0.3912,0.53819,254.58
> ui mousemode right "rotate selected models"
> ~select #7.1
Nothing selected
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
> includeMaps true
——— End of log from Tue Feb 22 21:54:19 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/2n5e.pdb"
2n5e.pdb title:
The 3D solution structure of discoidal high-density lipoprotein particles
[more info...]
Chain information for 2n5e.pdb
---
Chain | Description
8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.1/B 8.2/B 8.3/B
8.4/B 8.5/B 8.6/B 8.7/B 8.8/B 8.9/B 8.10/B | apolipoprotein A-I
> mmaker #8 to #7
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 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.1), sequence
alignment score = 889.9
RMSD between 167 pruned atom pairs is 0.000 angstroms; (across all 167 pairs:
0.000)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.2), sequence
alignment score = 889.9
RMSD between 99 pruned atom pairs is 0.967 angstroms; (across all 167 pairs:
2.405)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.3), sequence
alignment score = 882.7
RMSD between 146 pruned atom pairs is 0.614 angstroms; (across all 167 pairs:
6.590)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.4), sequence
alignment score = 879.1
RMSD between 90 pruned atom pairs is 0.877 angstroms; (across all 167 pairs:
6.733)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.5), sequence
alignment score = 886.3
RMSD between 83 pruned atom pairs is 0.781 angstroms; (across all 167 pairs:
7.288)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.6), sequence
alignment score = 889.9
RMSD between 150 pruned atom pairs is 0.625 angstroms; (across all 167 pairs:
4.094)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.7), sequence
alignment score = 886.3
RMSD between 150 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
2.428)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.8), sequence
alignment score = 882.7
RMSD between 114 pruned atom pairs is 1.220 angstroms; (across all 167 pairs:
8.487)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.9), sequence
alignment score = 886.3
RMSD between 137 pruned atom pairs is 0.954 angstroms; (across all 167 pairs:
7.152)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.10), sequence
alignment score = 886.3
RMSD between 149 pruned atom pairs is 0.855 angstroms; (across all 167 pairs:
1.629)
> close #7
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
> includeMaps true
——— End of log from Tue Feb 22 22:03:06 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb"
Chain information for ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb #7
---
Chain | Description
B C | No description available
> select #7
4272 atoms, 4342 bonds, 530 residues, 1 model selected
> view matrix models #7,1,0,0,155.3,0,1,0,-32.66,0,0,1,15.862
> view matrix models #7,1,0,0,227.55,0,1,0,182.45,0,0,1,257.42
> view matrix models #7,1,0,0,226.69,0,1,0,184.64,0,0,1,255.63
> view matrix models #7,1,0,0,204.58,0,1,0,234.23,0,0,1,235.65
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.67294,0.6481,-0.35654,204.55,-0.4966,0.03861,-0.86712,237.02,-0.54821,0.76058,0.34783,236.07
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.67294,0.6481,-0.35654,202.23,-0.4966,0.03861,-0.86712,223.37,-0.54821,0.76058,0.34783,214.9
> view matrix models
> #7,0.67294,0.6481,-0.35654,204.71,-0.4966,0.03861,-0.86712,212.44,-0.54821,0.76058,0.34783,207.19
> view matrix models
> #7,0.67294,0.6481,-0.35654,168.77,-0.4966,0.03861,-0.86712,212.73,-0.54821,0.76058,0.34783,213.42
> view matrix models
> #7,0.67294,0.6481,-0.35654,168.7,-0.4966,0.03861,-0.86712,204.73,-0.54821,0.76058,0.34783,218.41
> view matrix models
> #7,0.67294,0.6481,-0.35654,169.65,-0.4966,0.03861,-0.86712,208.53,-0.54821,0.76058,0.34783,221.42
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.74751,0.56918,-0.34243,169.65,-0.52825,0.19685,-0.82595,208.32,-0.40271,0.7983,0.44782,221.09
> view matrix models
> #7,0.17157,-0.18647,-0.96736,171.99,0.92678,0.36358,0.094287,205.38,0.33413,-0.91271,0.23519,222.64
> view matrix models
> #7,-0.43014,-0.90269,-0.011358,172.47,-0.7035,0.32728,0.63086,206.67,-0.56575,0.27935,-0.77582,223.35
> view matrix models
> #7,-0.56096,-0.12743,-0.81798,172.58,-0.79405,0.36224,0.48812,206.9,0.2341,0.92333,-0.30439,221.07
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,172.56,-0.84174,0.37778,0.38568,207.05,0.27385,0.91443,-0.29802,221.03
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,175.91,-0.84174,0.37778,0.38568,203.89,0.27385,0.91443,-0.29802,211.39
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,174.08,-0.84174,0.37778,0.38568,206.07,0.27385,0.91443,-0.29802,215.64
> hide #!8 models
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,174.65,-0.84174,0.37778,0.38568,206.88,0.27385,0.91443,-0.29802,212.06
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
> Ab56-apoa1.cxs" includeMaps true
——— End of log from Wed Mar 2 00:08:07 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb"
Chain information for ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb
#9
---
Chain | Description
B C | No description available
> mmaker #9 to #10
No 'to' model specified
> mmaker #9 to #7
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 ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb, chain B (#7) with
ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb, chain B (#9),
sequence alignment score = 1084.5
RMSD between 74 pruned atom pairs is 0.985 angstroms; (across all 207 pairs:
10.547)
> hide #7 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.52533,-0.58815,-0.61491,177.85,0.0047201,0.72466,-0.68909,201.87,0.85089,0.35909,0.38346,210.74
> view matrix models
> #9,0.45946,-0.88174,0.10689,181.58,0.8882,0.45638,-0.053134,204.22,-0.0019327,0.11935,0.99285,214.69
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.45946,-0.88174,0.10689,177.6,0.8882,0.45638,-0.053134,197.13,-0.0019327,0.11935,0.99285,218.41
> view matrix models
> #9,0.45946,-0.88174,0.10689,175.75,0.8882,0.45638,-0.053134,203.48,-0.0019327,0.11935,0.99285,218.85
> view matrix models
> #9,0.45946,-0.88174,0.10689,169.69,0.8882,0.45638,-0.053134,196.29,-0.0019327,0.11935,0.99285,214.81
> view matrix models
> #9,0.45946,-0.88174,0.10689,169.27,0.8882,0.45638,-0.053134,199.29,-0.0019327,0.11935,0.99285,212.88
> view matrix models
> #9,0.45946,-0.88174,0.10689,173.56,0.8882,0.45638,-0.053134,203.27,-0.0019327,0.11935,0.99285,212.35
> view matrix models
> #9,0.45946,-0.88174,0.10689,176.72,0.8882,0.45638,-0.053134,202,-0.0019327,0.11935,0.99285,212.91
> view matrix models
> #9,0.45946,-0.88174,0.10689,172.24,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.78
> view matrix models
> #9,0.45946,-0.88174,0.10689,171.54,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.45
> ui tool show "Fit in Map"
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 3334 atoms
average map value = 0.1014, steps = 288
shifted from previous position = 26.2
rotated from previous position = 35.6 degrees
atoms outside contour = 2236, contour level = 0.14151
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.15030095 -0.25689088 -0.95468145 159.80559539
0.91205850 0.40867945 0.03362089 142.63963221
0.38152180 -0.87577859 0.29572442 147.85545078
Axis -0.45590440 -0.66987165 0.58602316
Axis point -104.50370211 0.00000000 221.35941513
Rotation angle (degrees) 94.16607036
Shift along axis -81.75960077
> view matrix models
> #9,0.67727,-0.51922,0.52127,172.73,0.71543,0.63007,-0.30194,194.77,-0.17166,0.57742,0.7982,218.78
> view matrix models
> #9,0.67727,-0.51922,0.52127,173.99,0.71543,0.63007,-0.30194,197.51,-0.17166,0.57742,0.7982,212.36
> view matrix models
> #9,0.67727,-0.51922,0.52127,174.96,0.71543,0.63007,-0.30194,195,-0.17166,0.57742,0.7982,208.97
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.66193,-0.59819,0.45168,174.95,0.73725,0.62836,-0.24824,195.18,-0.13532,0.49732,0.85695,209.41
> view matrix models
> #9,0.64956,-0.67275,0.35424,174.82,0.71372,0.70012,0.020895,196.02,-0.26207,0.23925,0.93492,210.62
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
> Ab56-apoa1.cxs" includeMaps true
——— End of log from Wed Mar 2 00:18:18 2022 ———
opened ChimeraX session
> show #!1 models
> hide #!2 models
> hide #9 models
> hide #!10 models
> show #6 models
> hide #4 models
> hide #3 models
> ui tool show "Fit in Map"
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.07482, steps = 364
shifted from previous position = 2.61
rotated from previous position = 17.1 degrees
atoms outside contour = 8195, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99640848 0.07252019 0.04371456 331.26650068
-0.01695668 -0.67668277 0.73607941 166.80204366
0.08296151 0.73269451 0.67548215 -88.38561339
Axis -0.03462299 -0.40144391 -0.91522895
Axis point 169.54681270 98.35816249 0.00000000
Rotation angle (degrees) 177.19813771
Shift along axis 2.46197109
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.64956,-0.67275,0.35424,175.54,0.71372,0.70012,0.020895,189.47,-0.26207,0.23925,0.93492,190.81
> ~select #9
Nothing selected
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> view matrix models
> #6,-0.99797,0.039575,0.049905,338.25,-0.014392,-0.90338,0.42859,266.52,0.062045,0.42701,0.90212,-62.663
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.99623,0.082033,0.028348,334.24,-0.086585,-0.91673,-0.39002,429.14,-0.006007,-0.391,0.92037,92.117
> view matrix models
> #6,-0.99623,0.082033,0.028348,335.42,-0.086585,-0.91673,-0.39002,430.38,-0.006007,-0.391,0.92037,88.929
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.09493, steps = 84
shifted from previous position = 3.13
rotated from previous position = 3.82 degrees
atoms outside contour = 7003, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99820989 0.05968746 0.00379835 345.43779112
-0.05973880 -0.99809742 -0.01525811 372.27574829
0.00288041 -0.01545771 0.99987637 1.80150722
Axis -0.00167123 0.00768605 -0.99996907
Axis point 178.28007958 180.98306790 0.00000000
Rotation angle (degrees) 176.57654715
Shift along axis 0.48257203
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.09495, steps = 48
shifted from previous position = 0.019
rotated from previous position = 0.00432 degrees
atoms outside contour = 7012, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99820895 0.05970074 0.00383565 345.40975009
-0.05975246 -0.99809759 -0.01519388 372.26991158
0.00292127 -0.01539585 0.99987721 1.78218185
Axis -0.00169079 0.00765450 -0.99996927
Axis point 178.26722509 180.97930211 0.00000000
Rotation angle (degrees) 176.57577490
Shift along axis 0.48339683
> set bgColor white
> lighting full
> ~select #6
Nothing selected
> hide #6 models
> show #6 models
> color #6 bychain
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> select #1
2 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> ~select #1
Nothing selected
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #3 models
> show #4 models
> hide #6 models
> volume #2 color #a7a49f80
> volume #2 color #b8b5af80
> color #3-4 bychain
Color zone shortcut requires 1 displayed atomic model and 1 map, got 12 atomic
models, 1 maps.
> hide #4 models
> show #4 models
> hide #4 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select #2
2 models selected
> ~select #2
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> show #4 models
> ui tool show "Segment Map"
> show #9 models
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.64956,-0.67275,0.35424,173.28,0.71372,0.70012,0.020895,203.74,-0.26207,0.23925,0.93492,217.24
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.42545,-0.83111,0.35811,174.01,0.88507,0.46469,0.026952,204.31,-0.18881,0.30548,0.93329,216.96
> view matrix models
> #9,0.36854,-0.89204,0.26163,173.89,0.89839,0.4141,0.14638,204.91,-0.23892,0.18109,0.954,217.47
> view matrix models
> #9,0.39748,-0.85333,0.3374,174.03,0.89601,0.44024,0.057848,204.49,-0.1979,0.27932,0.93958,217.07
> view matrix models
> #9,0.4249,-0.82293,0.37715,174.06,0.89397,0.44699,-0.03185,204.13,-0.14237,0.3507,0.9256,216.74
> view matrix models
> #9,0.30959,-0.88763,0.34097,174.24,0.94929,0.30918,-0.057041,204.4,-0.05479,0.34134,0.93834,216.73
> ~select #9
Nothing selected
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.30959,-0.88763,0.34097,171.78,0.94929,0.30918,-0.057041,200.45,-0.05479,0.34134,0.93834,215.77
> ~select #9
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\dahailuo\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\movie2.mp4"
Movie saved to \C:Users\\...\Data_EM_Alvin\movie2.mp4
> show #6 models
> mmaker #6 to #3
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 D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> mmaker #6 to #4
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 F562a.pdb, chain B (#4) with D2NS1-F562.pdb, chain C (#6), sequence
alignment score = 1200
RMSD between 228 pruned atom pairs is 0.000 angstroms; (across all 228 pairs:
0.000)
> hide #!2 models
> hide #9 models
> hide #3 models
> hide #4 models
> show #!2 models
> hide #6 models
> show #!1 models
> show #!10 models
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 48, shift = 0.0601, angle = 0.109 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27792284 -0.14164293 -0.95010322 410.09306464
0.39540197 0.88452622 -0.24752902 -48.83916554
0.87545196 -0.44446666 -0.18982414 109.38604242
Axis -0.10294301 -0.95425209 0.28072349
Axis point 169.05771360 0.00000000 208.04394464
Rotation angle (degrees) 106.95439226
Shift along axis 35.09589160
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2809, overlap = 5991
steps = 48, shift = 0.0078, angle = 0.0885 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27794843 -0.14312388 -0.94987377 410.31424613
0.39534589 0.88416435 -0.24890760 -48.51539453
0.87546917 -0.44471217 -0.18916865 109.30275225
Axis -0.10234637 -0.95410041 0.28145627
Axis point 169.16249688 0.00000000 208.15543264
Rotation angle (degrees) 106.94636481
Shift along axis 35.05832906
> hide #!2 models
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.74046,0.62541,0.24616,-107.44,-0.65719,0.75044,0.070241,152.95,-0.1408,-0.21378,0.96668,70.267
> view matrix models
> #1,0.72193,-0.13867,0.67793,-42.597,0.2204,0.97477,-0.035306,-25.414,-0.65593,0.1749,0.73428,133.11
> view matrix models
> #1,0.74615,0.64297,-0.17276,-38.999,0.62682,-0.76589,-0.14322,231.4,-0.22441,-0.0014231,-0.97449,383.68
> view matrix models
> #1,0.80841,0.29993,0.50648,-106.59,0.51816,-0.77083,-0.37058,291.07,0.27926,0.56202,-0.77856,159.28
> view matrix models
> #1,0.96135,-0.23483,0.14371,24.411,0.25186,0.96097,-0.11451,-14.839,-0.11121,0.14628,0.98297,-2.0945
> view matrix models
> #1,0.99141,-0.075528,-0.10677,34.022,0.051461,0.97582,-0.21244,35.244,0.12024,0.20512,0.97132,-51.881
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 716, shift = 1.66, angle = 12.6 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27785362 -0.14026525 -0.95032783 409.88132947
0.39567157 0.88475643 -0.24627224 -49.16134094
0.87535212 -0.44444535 -0.19033380 109.50506725
Axis -0.10359229 -0.95434929 0.28015367
Axis point 168.94433960 0.00000000 207.96495201
Rotation angle (degrees) 106.96068830
Shift along axis 35.13479072
> show #!2 models
> hide #!2 models
> show #!2 models
> ~select #1
Nothing selected
> select #1
2 models selected
> view matrix models
> #1,0.9987,0.030982,-0.040533,2.2432,0.0036821,0.74864,0.66296,-67.414,0.050884,-0.66225,0.74755,154.04
> view matrix models
> #1,0.87306,0.20075,-0.44437,64.348,0.48063,-0.20061,0.85367,-16.172,0.082229,-0.95888,-0.27163,378
> view matrix models
> #1,0.83244,0.37492,-0.40802,34.215,0.55119,-0.48475,0.67912,52.19,0.056831,-0.79023,-0.61017,411.1
> view matrix models
> #1,0.68639,0.56283,-0.46053,35.845,0.69489,-0.69435,0.1871,149.22,-0.21447,-0.44844,-0.8677,443.15
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> view matrix models
> #1,0.82844,0.50873,-0.23428,-19.057,0.47101,-0.40647,0.7829,34.547,0.30305,-0.75893,-0.57635,355.71
> view matrix models
> #1,0.84453,-0.094928,-0.52703,136.53,-0.025459,-0.99017,0.13755,339.15,-0.5349,-0.10275,-0.83864,433.6
> view matrix models
> #1,0.97799,-0.18464,-0.097184,54.238,-0.1969,-0.66248,-0.72274,460.34,0.069068,0.72597,-0.68425,151.17
> view matrix models
> #1,0.97796,-0.19168,-0.082782,53.003,-0.16644,-0.47632,-0.86337,446.06,0.12606,0.85812,-0.49773,85.086
> view matrix models
> #1,0.99726,0.035713,-0.06472,5.846,-0.039623,-0.48086,-0.8759,426.41,-0.062402,0.87607,-0.47813,112.12
> view matrix models
> #1,-0.96752,0.24305,-0.069446,320.31,-0.20699,-0.60408,0.76957,193.12,0.14509,0.75896,0.63477,-96.862
> view matrix models
> #1,-0.85416,0.24266,-0.45992,367.81,-0.51768,-0.48048,0.70792,237.19,-0.049202,0.84277,0.53603,-60.033
> view matrix models
> #1,-0.98697,0.14048,-0.078425,343.64,-0.16057,-0.82904,0.53564,265.52,0.010232,0.54125,0.8408,-69.644
> view matrix models
> #1,-0.99016,0.10292,-0.094853,353.76,-0.13794,-0.83244,0.53668,261.91,-0.023726,0.54448,0.83844,-63.751
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99016,0.10292,-0.094853,357.93,-0.13794,-0.83244,0.53668,248.71,-0.023726,0.54448,0.83844,-68.308
> view matrix models
> #1,-0.99016,0.10292,-0.094853,358.29,-0.13794,-0.83244,0.53668,250.68,-0.023726,0.54448,0.83844,-68.894
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.9422,-0.030752,0.33364,299.34,0.13856,-0.9424,0.30443,261.21,0.30506,0.33307,0.89219,-99.156
> view matrix models
> #1,-0.77548,-0.32284,0.54259,285.5,0.28029,-0.94609,-0.16233,317.46,0.56574,0.026196,0.82416,-79.125
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.77548,-0.32284,0.54259,268.3,0.28029,-0.94609,-0.16233,334.8,0.56574,0.026196,0.82416,-67.645
> view matrix models
> #1,-0.77548,-0.32284,0.54259,265.58,0.28029,-0.94609,-0.16233,338.57,0.56574,0.026196,0.82416,-65.98
> view matrix models
> #1,-0.77548,-0.32284,0.54259,285.03,0.28029,-0.94609,-0.16233,352.61,0.56574,0.026196,0.82416,-59.271
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.91194,-0.17978,0.36883,313.96,0.10929,-0.97286,-0.20397,395.12,0.39549,-0.1457,0.90684,-12.537
> view matrix models
> #1,-0.91113,-0.10679,0.39805,295.73,0.021642,-0.97691,-0.21254,412.97,0.41156,-0.18504,0.8924,-5.8812
> view matrix models
> #1,-0.99135,-0.088862,0.096564,359.09,0.037913,-0.89841,-0.43753,435.05,0.12563,-0.43008,0.894,88.599
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99135,-0.088862,0.096564,361.35,0.037913,-0.89841,-0.43753,415.99,0.12563,-0.43008,0.894,90.946
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99008,-0.020034,0.1391,341.47,-0.013738,-0.97125,-0.23766,403.58,0.13986,-0.23721,0.96134,42.319
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99008,-0.020034,0.1391,341.46,-0.013738,-0.97125,-0.23766,399.55,0.13986,-0.23721,0.96134,42.616
> view matrix models
> #1,-0.99008,-0.020034,0.1391,338.93,-0.013738,-0.97125,-0.23766,400.44,0.13986,-0.23721,0.96134,32.494
> view matrix models
> #1,-0.99008,-0.020034,0.1391,335.49,-0.013738,-0.97125,-0.23766,400.28,0.13986,-0.23721,0.96134,33.65
> view matrix models
> #1,-0.99008,-0.020034,0.1391,333.14,-0.013738,-0.97125,-0.23766,400.18,0.13986,-0.23721,0.96134,33.756
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99347,-0.11227,0.020092,370.83,0.11149,-0.99309,-0.036498,346.87,0.024051,-0.03402,0.99913,11.612
> view matrix models
> #1,-0.99314,-0.11513,0.02023,371.26,0.11367,-0.99155,-0.06254,350.72,0.027259,-0.059812,0.99784,15.866
> view matrix models
> #1,-0.99502,-0.048682,0.086949,348.18,0.043004,-0.99689,-0.06602,364.89,0.089893,-0.061952,0.99402,5.7314
> view matrix models
> #1,-0.9999,-0.011841,0.0079016,356.17,0.012535,-0.99545,0.094484,342.25,0.0067469,0.094574,0.9955,-7.6193
> view matrix models
> #1,-0.99955,0.029264,0.006465,349.02,-0.028596,-0.99584,0.086513,351.05,0.0089699,0.086289,0.99623,-6.6648
> show #!2 models
> hide #!2 models
> view matrix models
> #1,-0.99431,-0.012476,0.10579,338.32,0.013343,-0.99988,0.0074894,357.98,0.10568,0.0088583,0.99436,-9.7821
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 948, shift = 10.3, angle = 23.5 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.27780939 0.13998726 -0.95038174 260.70800172
-0.39575740 -0.88479067 -0.24601119 407.82841194
-0.87532735 0.44446484 -0.19040216 263.31428797
Axis 0.78717074 -0.08556506 -0.61077070
Axis point 0.00000000 178.59809032 292.75645151
Rotation angle (degrees) 153.98663078
Shift along axis 9.50119898
> hide #!10 models
> show #6 models
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> ~select #6
Nothing selected
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> view matrix models
> #6,0.80584,-0.033933,0.59116,-60.641,-0.18803,0.93202,0.30982,-22.728,-0.56149,-0.36082,0.74468,228.14
> view matrix models
> #6,0.84169,0.23741,0.48497,-96.336,-0.031206,0.91804,-0.39525,78.603,-0.53906,0.31754,0.78012,96.759
> view matrix models
> #6,0.95752,0.28708,0.027255,-43.538,-0.26323,0.90873,-0.32391,108.93,-0.11776,0.30298,0.94569,-5.8011
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.95752,0.28708,0.027255,-47.959,-0.26323,0.90873,-0.32391,118,-0.11776,0.30298,0.94569,-22.337
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99918,0.040001,0.0063686,-7.5857,-0.036305,0.95416,-0.29708,64.472,-0.01796,0.2966,0.95483,-40.695
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 96
shifted from previous position = 4.3
rotated from previous position = 4.93 degrees
atoms outside contour = 6857, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 -0.00003889 0.00000390 356.92132489
0.00003889 -0.99999983 -0.00059770 357.02795185
0.00000392 -0.00059770 0.99999983 0.10572384
Axis -0.00000446 -0.00030232 0.99999995
Axis point 178.45719114 178.51746241 0.00000000
Rotation angle (degrees) 179.99777155
Shift along axis -0.00380630
> ~select #6
Nothing selected
> interfaces #6 & ~solvent
7 buried areas: A B 2354, E F 2040, C D 2040, B C 1572, A F 1542, B D 1312, A
E 1190
> open "C:/Users/dahailuo/Downloads/cryosparc_P35_J100_005_volume_map_sharp
> (1).mrc"
Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
416,416,416, pixel 0.858, shown at level 0.0415, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1102+1920+23 (frame:
1936x1141+1912-8) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1920x1017+1920+23 (frame:
1936x1056+1912-8) margins: 8, 31, 8, 8 minimum size: 493x1102 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=509,1141 maxtrack=0,0)
> volume #11 step 1
> surface dust #1 size 8.58
> surface dust #11 size 8.58
> volume #11 level 0.045
> volume #11 level 0.05
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) using 12404 atoms
average map value = 0.08442, steps = 152
shifted from previous position = 1.4
rotated from previous position = 4.71 degrees
atoms outside contour = 5898, contour level = 0.05
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) coordinates:
Matrix rotation and translation
0.99897026 0.04182548 -0.01757995 -4.15590074
-0.04516063 0.95385198 -0.29686178 69.02604187
0.00435228 0.29735001 0.95475862 -45.20466997
Axis 0.98879513 -0.03649622 -0.14474879
Axis point 0.00000000 183.11150795 204.04343868
Rotation angle (degrees) 17.48599398
Shift along axis -0.08520266
> transparency #11.1 50
> show #3 models
> mmaker #3 to #6
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 D2NS1-F562.pdb, chain A (#6) with D2NS1.pdb, chain B (#3), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07338, steps = 60
shifted from previous position = 1.1
rotated from previous position = 2.61 degrees
atoms outside contour = 3025, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14875593 -0.08639183 -0.98509297 342.36735832
0.98470147 -0.07847453 0.15557896 -15.12271804
-0.09074546 -0.99316577 0.07339661 361.18209695
Axis -0.63557683 -0.49482408 0.59261389
Axis point 0.00000000 37.80172615 346.76474569
Rotation angle (degrees) 115.35090835
Shift along axis 3.92385104
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07339, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.00688 degrees
atoms outside contour = 3021, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14885535 -0.08637602 -0.98507934 342.35458834
0.98468094 -0.07852972 0.15568097 -15.13336069
-0.09080510 -0.99316278 0.07336326 361.19655370
Axis -0.63562980 -0.49478213 0.59259210
Axis point 0.00000000 37.81870419 346.75288311
Rotation angle (degrees) 115.35056364
Shift along axis 3.91916090
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07338, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.0195 degrees
atoms outside contour = 3027, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14869429 -0.08663603 -0.98508083 342.41395707
0.98471526 -0.07839157 0.15553350 -15.12882419
-0.09069683 -0.99315105 0.07365544 361.12491138
Axis -0.63549687 -0.49480794 0.59271311
Axis point 0.00000000 37.79183158 346.80910583
Rotation angle (degrees) 115.34202749
Shift along axis 3.92633355
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,0.052602,-0.042076,-0.99773,354.08,0.96197,-0.26603,0.061936,37.093,-0.26803,-0.96305,0.026482,395.65
> view matrix models
> #3,0.0070452,-0.012575,-0.9999,357.51,0.93425,-0.35645,0.011066,66.236,-0.35656,-0.93423,0.0092369,409.45
> view matrix models
> #3,-0.0058622,0.0073093,-0.99996,356.45,0.91272,-0.40851,-0.0083368,82.232,-0.40855,-0.91272,-0.0042765,417.39
> view matrix models
> #3,-0.020074,-0.027951,-0.99941,364.78,0.92365,-0.38315,-0.0078364,75.954,-0.3827,-0.92326,0.033508,407.88
> view matrix models
> #3,0.0017745,-0.041136,-0.99915,363.11,0.92163,-0.38766,0.017597,72.537,-0.38806,-0.92088,0.037224,407.76
> view matrix models
> #3,-0.017771,-0.12129,-0.99246,378.83,0.9086,-0.41622,0.034596,76.603,-0.41728,-0.90114,0.1176,395.26
> view matrix models
> #3,0.012861,-0.10916,-0.99394,371.67,0.88601,-0.45952,0.061933,82.986,-0.46349,-0.88144,0.09081,404.85
> view matrix models
> #3,0.012034,-0.092833,-0.99561,369.37,0.88338,-0.46553,0.054084,85.858,-0.46851,-0.88015,0.076405,408.08
> view matrix models
> #3,0.022255,-0.099641,-0.99477,368.56,0.88274,-0.46516,0.066341,83.724,-0.46934,-0.8796,0.077605,407.92
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.022255,-0.099641,-0.99477,369.16,0.88274,-0.46516,0.066341,83.998,-0.46934,-0.8796,0.077605,407.23
> view matrix models
> #3,0.022255,-0.099641,-0.99477,368.06,0.88274,-0.46516,0.066341,83.639,-0.46934,-0.8796,0.077605,407.78
> view matrix models
> #3,0.022255,-0.099641,-0.99477,369.91,0.88274,-0.46516,0.066341,85.463,-0.46934,-0.8796,0.077605,407.43
> ~select #3
Nothing selected
> show #6 models
> mmaker #6 to #3
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 D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> show #4 models
> hide #4 models
> show #4 models
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1004, steps = 64
shifted from previous position = 1.84
rotated from previous position = 3.05 degrees
atoms outside contour = 1419, contour level = 0.05
Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.82616267 0.51307542 -0.23282799 17.45941536
-0.12390784 -0.23766697 -0.96341127 357.00880636
-0.54963816 0.82478363 -0.13277751 149.37621508
Axis 0.92916660 0.16461820 -0.33098381
Axis point 0.00000000 112.71394709 221.40097809
Rotation angle (degrees) 105.79170262
Shift along axis 25.55174348
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1004, steps = 48
shifted from previous position = 0.011
rotated from previous position = 0.0276 degrees
atoms outside contour = 1418, contour level = 0.05
Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.82596970 0.51342982 -0.23273140 17.41926576
-0.12364669 -0.23778983 -0.96341451 356.97717269
-0.54998689 0.82452765 -0.13292329 149.51361297
Axis 0.92909832 0.16486078 -0.33105473
Axis point 0.00000000 112.65571575 221.42366392
Rotation angle (degrees) 105.80544612
Shift along axis 25.53855668
> hide #6 models
> show #5 models
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1083, steps = 76
shifted from previous position = 0.951
rotated from previous position = 3.36 degrees
atoms outside contour = 1258, contour level = 0.05
Position of F562b.pdb (#5) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.91100184 -0.19027699 -0.36588295 82.97740999
-0.38499639 -0.71041595 -0.58914087 517.50161240
-0.14782913 0.67757202 -0.72044619 248.76959820
Axis 0.97438742 -0.16773248 -0.14978305
Axis point 0.00000000 219.97208546 227.46670853
Rotation angle (degrees) 139.45804049
Shift along axis -43.21115606
> color #3-5 bychain
> hide #!11 models
> save "C:/Users/dahailuo/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab56
> .cxs"
> save "C:/Users/dahailuo/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-
> Fab5-DL.cxs" includeMaps true
——— End of log from Thu Mar 3 12:01:46 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #5
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #7 models
> hide #!8 models
> hide #9 models
> close #8
> show #9 models
> hide #9 models
> show #7 models
> show #9 models
> hide #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:9-11
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B:1-207
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-86
208 atoms, 215 bonds, 23 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an
ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-
tuples-or ndarrays with different lengths or shapes) is deprecated. If you
meant to do this, you must specify 'dtype=object' when creating the ndarray
return array(a, dtype, copy=False, order=order)
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
> color sel blue
> color sel cornflower blue
> select #9/B:151-152
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #9/B:151-172
163 atoms, 164 bonds, 22 residues, 1 model selected
> color sel cornflower blue
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> close #10
> close #11
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #3 models
> show #4 models
> show #5 models
> hide #5 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> hide #4 models
> show #4 models
> hide #4 models
> select #9/C:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/C:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
> color sel medium blue
> select #9/C:151
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/C:151-172
163 atoms, 164 bonds, 22 residues, 1 model selected
> color sel medium blue
> close #7
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> close #6
> show #4 models
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J142_005_volume_map_sharp.mrc"
Opened cryosparc_P47_J142_005_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 0.85, shown at level 0.0449, step 2, values float32
> volume #6 step 1
> volume #6 level 0.1656
> volume #6 level 0.06061
> close #6
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J128_002_volume_map_sharp.mrc"
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 0.85, shown at level 0.0566, step 2, values float32
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #!6 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> show #!6 models
> volume #6 step 1
> volume #6 level 0.116
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J132_002_volume_map_sharp.mrc"
Opened cryosparc_P47_J132_002_volume_map_sharp.mrc as #7, grid size
360,360,360, pixel 0.85, shown at level 0.0558, step 2, values float32
> volume #7 step 1
> volume #7 level 0.189
> volume #6 level 0.148
> volume #6 level 0.1384
> volume #7 level 0.08193
> volume #7 level 0.04862
> volume #6 level 0.06462
> close #7
> volume #6 level 0.1336
> volume #6 level 0.1256
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #6
2 models selected
> view matrix models
> #6,-0.83996,0.011508,0.54253,184.02,0.50426,0.3859,0.77253,-105.68,-0.20047,0.92247,-0.32995,103.36
> view matrix models
> #6,0.1848,-0.18014,0.96613,-8.4193,0.46665,-0.84908,-0.24758,260.82,0.86492,0.4966,-0.072852,-31.125
> view matrix models
> #6,0.25195,-0.19005,0.94889,-14.067,0.4832,-0.82485,-0.29351,262.08,0.83847,0.53245,-0.11599,-25.726
> view matrix models
> #6,-0.035938,-0.13733,0.98987,13.939,0.38333,-0.91664,-0.11325,261.83,0.92291,0.37538,0.085583,-46.756
> view matrix models
> #6,0.1558,-0.53982,0.82724,75.077,-0.30263,-0.82328,-0.48024,409.8,0.94029,-0.17552,-0.29163,98.871
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.1558,-0.53982,0.82724,121.85,-0.30263,-0.82328,-0.48024,428.76,0.94029,-0.17552,-0.29163,116.7
> view matrix models
> #6,0.1558,-0.53982,0.82724,122.7,-0.30263,-0.82328,-0.48024,438.5,0.94029,-0.17552,-0.29163,113.43
> view matrix models
> #6,0.1558,-0.53982,0.82724,123.68,-0.30263,-0.82328,-0.48024,449.46,0.94029,-0.17552,-0.29163,118.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.15847,-0.55227,0.81847,126.67,-0.30396,-0.81597,-0.49173,450.39,0.93941,-0.17086,-0.29717,118.9
> view matrix models
> #6,0.31733,-0.49565,0.80848,95.704,-0.41983,-0.83787,-0.34888,447.71,0.85032,-0.22872,-0.47397,170.26
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.921,-0.41983,-0.83787,-0.34888,440.31,0.85032,-0.22872,-0.47397,180.5
> view matrix models
> #6,0.31733,-0.49565,0.80848,96.096,-0.41983,-0.83787,-0.34888,439.7,0.85032,-0.22872,-0.47397,180.02
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.946,-0.41983,-0.83787,-0.34888,439.56,0.85032,-0.22872,-0.47397,179.06
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.851,-0.41983,-0.83787,-0.34888,439.42,0.85032,-0.22872,-0.47397,178.96
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.32806,-0.48111,0.81296,90.235,-0.37939,-0.85524,-0.35303,436.79,0.86512,-0.19262,-0.4631,169.31
> view matrix models
> #6,0.36269,-0.41122,0.83627,70.284,-0.30986,-0.89953,-0.30795,425.95,0.87889,-0.14743,-0.45367,158.62
> view matrix models
> #6,0.36637,-0.44198,0.8188,77.421,-0.35476,-0.87986,-0.31621,430.93,0.86019,-0.17462,-0.47915,169.85
> view matrix models
> #6,0.36072,-0.39988,0.8426,67.762,-0.30034,-0.9051,-0.30097,424.26,0.88299,-0.1445,-0.44659,156.39
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.36072,-0.39988,0.8426,67.7,-0.30034,-0.9051,-0.30097,421.64,0.88299,-0.1445,-0.44659,155.81
> view matrix models
> #6,0.36072,-0.39988,0.8426,69.281,-0.30034,-0.9051,-0.30097,420.24,0.88299,-0.1445,-0.44659,157.09
> view matrix models
> #6,0.36072,-0.39988,0.8426,69.528,-0.30034,-0.9051,-0.30097,421,0.88299,-0.1445,-0.44659,156.78
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.36427,-0.41429,0.83407,72.656,-0.28999,-0.90154,-0.32115,422.2,0.88499,-0.12489,-0.44854,153.73
> view matrix models
> #6,0.35177,-0.40975,0.84164,72.569,-0.29057,-0.90249,-0.31793,421.91,0.88984,-0.13272,-0.43653,152.26
> view matrix models
> #6,0.3599,-0.44231,0.82148,79.767,-0.28748,-0.89021,-0.35338,425.33,0.8876,-0.10898,-0.44754,150.68
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.749,-0.29539,-0.89136,-0.34382,425.13,0.87766,-0.11101,-0.46626,155.55
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.37744,-0.43949,0.8151,76.75,-0.29539,-0.89136,-0.34382,424.99,0.87766,-0.11101,-0.46626,155.59
> view matrix models
> #6,0.37744,-0.43949,0.8151,75.665,-0.29539,-0.89136,-0.34382,426.6,0.87766,-0.11101,-0.46626,156.42
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.299,-0.29539,-0.89136,-0.34382,425.99,0.87766,-0.11101,-0.46626,155.38
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.803,-0.29539,-0.89136,-0.34382,426.26,0.87766,-0.11101,-0.46626,155.31
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.3964,-0.4154,0.81873,70.6,-0.31009,-0.89996,-0.30647,423.68,0.86412,-0.13239,-0.48555,163.85
> view matrix models
> #6,0.36188,-0.4339,0.82509,77.612,-0.3531,-0.88293,-0.30945,427.92,0.86276,-0.17936,-0.47273,169.32
> view matrix models
> #6,0.34333,-0.43629,0.83173,79.67,-0.33947,-0.88333,-0.32323,428.21,0.87572,-0.17137,-0.45138,162.63
> view matrix models
> #6,0.36882,-0.43654,0.82061,77.724,-0.34143,-0.88476,-0.31721,427.74,0.86452,-0.16319,-0.47537,166.95
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.88,-0.33111,-0.89091,-0.31088,426.13,0.86644,-0.15658,-0.47409,165.42
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.37369,-0.42634,0.82377,75.079,-0.33111,-0.89091,-0.31088,425.43,0.86644,-0.15658,-0.47409,165.61
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.521,-0.33111,-0.89091,-0.31088,425.67,0.86644,-0.15658,-0.47409,165.89
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.154,-0.33111,-0.89091,-0.31088,425.74,0.86644,-0.15658,-0.47409,166.14
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.447,-0.33111,-0.89091,-0.31088,425.75,0.86644,-0.15658,-0.47409,166.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.5154,-0.37111,0.77242,53.045,-0.24207,-0.9277,-0.2842,413.84,0.82205,-0.040509,-0.56797,170.41
> view matrix models
> #6,0.49373,-0.37696,0.78367,55.354,-0.26058,-0.92389,-0.28024,415.36,0.82966,-0.065846,-0.55437,171.02
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ~select #6
Nothing selected
> vop resample #6 onGrid #2
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> close #6
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> volume #7 level 0.09689
Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 175454 points
correlation = 0.8828, correlation about mean = 0.547, overlap = 7225
steps = 168, shift = 7.84, angle = 17 degrees
Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.95949380 0.09544158 -0.26507085 39.26017660
-0.07373087 0.99314477 0.09070403 -7.34539260
0.27191066 -0.06748605 0.95995324 -23.66014125
Axis -0.27050228 -0.91822900 -0.28928192
Axis point 103.77985456 0.00000000 135.28320696
Rotation angle (degrees) 17.00173416
Shift along axis 2.96923623
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, 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
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_ac.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, 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
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 8 GB
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 1 day 21:10
Graphics/Displays:
Apple G13G:
Chipset Model: Apple G13G
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
CB242Y:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (1)
comment:1 by , 4 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Region not in region_browser.sequence_regions |
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Use region.browser.delete_region() rather than region.destroy() directly