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Opened 4 years ago
Closed 4 years ago
#4830 closed defect (duplicate)
MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
matchmaker for alignment between 12 monomers in biological assembly dodecamer and 12 monomers in another biological assembly dedeacmer
The matchmatker
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
Log from Sun Jun 27 06:44:30 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job027/run_it019_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job027/run_it019_class004.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job027/run_it019_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job027/run_it019_class002.mrc
Opened run_it019_class001.mrc, grid size 480,480,480, pixel 0.83, shown at
level 0.00289, step 2, values float32
> volume #1.2 level 0.004745
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job016/run_it025_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job016/run_it025_class002.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job016/run_it025_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job016/run_it025_class004.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00697, step 2, values float32
> close session
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job028/run_it025_class001.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00686, step 2, values float32
> volume #1 level 0.007141
> volume #1 level 0.005285
> volume #1 level 0.007786
> close session
> open /Users/hchou01/temp/Refine3D/arctica/job038/run_ct13_class001_320p.mrc
Opened run_ct13_class001_320p.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00524, step 2, values float32
> volume #1 level 0.008905
> open /Users/hchou01/temp/Refine3D/arctica/job038/3unit.pdb
Chain information for 3unit.pdb #2
---
Chain | Description
A | No description available
> open /Users/hchou01/temp/Refine3D/arctica/job038/run_ct13_class001.mrc
Opened run_ct13_class001.mrc, grid size 480,480,480, pixel 0.83, shown at
level 0.00257, step 2, values float32
> close session
> open /Users/hchou01/temp/Refine3D/arctica/job058/run_ct18_class001.mrc
Opened run_ct18_class001.mrc, grid size 480,480,480, pixel 0.83, shown at
level 0.00211, step 2, values float32
> volume #1 step 1
> volume #1 level 0.009332
> open /Users/hchou01/temp/Refine3D/arctica/job038/run_ct13_class001_320p.mrc
Opened run_ct13_class001_320p.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00524, step 2, values float32
> volume #2 step 1
> volume #2 level 0.009769
> volume #1 level 0.01115
> open /Users/hchou01/temp/LD-
> CAMK2D-CaM/Refine3D/run_ct4_it010_half1_class001.mrc /Users/hchou01/temp/LD-
> CAMK2D-CaM/Refine3D/run_ct4_it010_half2_class001.mrc
Opened run_ct4_it010_half1_class001.mrc, grid size 320,320,320, pixel 0.83,
shown at level 0.00685, step 2, values float32
> volume #3.1 level 0.007664
> volume #2 level 0.01086
> close session
> ui tool show "Fit in Map"
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job016/hubs-1kinase_align.mrc
Opened hubs-1kinase_align.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 2, values float32
> open /Users/hchou01/temp/LD-CAMK2D-CaM/volume_16_2.mrc
Opened volume_16_2.mrc, grid size 320,320,320, pixel 0.83, shown at level
1.04, step 2, values float32
> volume #2 level 2.129
> volume #1 step 1
> volume #2 step 1
> volume #2 level 2.924
> volume #1 level 0.02249
> volume #2 level 1.757
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class002.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class004.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00488, step 2, values float32
> hide #!3 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class002.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class004.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00488, step 2, values float32
> close session
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class002.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job014/run_it025_class004.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00488, step 2, values float32
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.1 models
> close session
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Refine3D/run_ct4_class001.mrc
Opened run_ct4_class001.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.00674, step 2, values float32
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job016/hubs-1kinase_align.mrc
Opened hubs-1kinase_align.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #2 level 0.0253
> ui tool show "Fit in Map"
Fit map run_ct4_class001.mrc in map hubs-1kinase_align.mrc using 327555 points
correlation = 0.8711, correlation about mean = 0.6874, overlap = 94.31
steps = 60, shift = 0.443, angle = 1.62 degrees
Position of run_ct4_class001.mrc (#1) relative to hubs-1kinase_align.mrc (#2)
coordinates:
Matrix rotation and translation
0.99967316 0.00524644 -0.02502107 2.98980430
-0.00554350 0.99991480 -0.01181762 2.35239284
0.02495694 0.01195246 0.99961707 -5.13064631
Axis 0.42156931 -0.88637442 -0.19136276
Axis point 206.12667794 0.00000000 114.15158657
Rotation angle (degrees) 1.61551838
Shift along axis 0.15712351
Fit map hubs-1kinase_align.mrc in map run_ct4_class001.mrc using 134956 points
correlation = 0.9482, correlation about mean = 0.5052, overlap = 75.96
steps = 64, shift = 0.447, angle = 1.61 degrees
Position of hubs-1kinase_align.mrc (#2) relative to run_ct4_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99966829 -0.00597965 0.02505118 -2.78822936
0.00569272 0.99991756 0.01150956 -2.29876751
-0.02511794 -0.01136314 0.99961991 5.15936220
Axis -0.40583884 0.89016935 0.20710712
Axis point 202.45010937 0.00000000 111.49011390
Rotation angle (degrees) 1.61478211
Shift along axis 0.15382005
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/2wel.pdb
2wel.pdb title:
Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase
II δ In complex with calmodulin [more info...]
Chain information for 2wel.pdb #3
---
Chain | Description
A | calcium/calmodulin-dependent protein kinase type II δ chain
D | CAM
Non-standard residues in 2wel.pdb #3
---
CA — calcium ion
EDO — 1,2-ethanediol (ethylene glycol)
K88 —
(3Z)-N,N-dimethyl-2-oxo-3-(4,5,6,7-tetrahydro-1H-indol-2-ylmethylidene)-2,3-dihydro-1H-indole-5-sulfonamide
PO4 — phosphate ion
> select #3
4013 atoms, 3666 bonds, 30 pseudobonds, 867 residues, 3 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select /D
1235 atoms, 1135 bonds, 28 pseudobonds, 257 residues, 2 models selected
> select #3.2
2 pseudobonds, 1 model selected
> ~select #3.2
Nothing selected
> select #3.1
28 pseudobonds, 1 model selected
> ~select #3.1
Nothing selected
> select /D
1235 atoms, 1135 bonds, 28 pseudobonds, 257 residues, 2 models selected
> volume #1 level 0.008811
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/3soa.pdb
3soa.pdb title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb #4
---
Chain | Description
A | calcium/calmodulin-dependent protein kinase type II subunit α with A β 7
linker
Non-standard residues in 3soa.pdb #4
---
DB8 —
4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
(bosutinib)
> close #4
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/3soa.pdb1
3soa.pdb1 title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb1
---
Chain | Description
4.1/A | No description available
4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A | No
description available
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ~select #4
Nothing selected
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ~select #4
Nothing selected
> hide #!4 models
> volume #1 level 0.007971
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job032/run_it017_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job032/run_it017_class002.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job032/run_it017_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job032/run_it017_class004.mrc
Opened run_it017_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00689, step 2, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #3.1 models
> hide #3.2 models
> hide #!5 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> hide #!5.4 models
> show #!5.4 models
> hide #!5.4 models
> show #!5.3 models
> hide #!5.3 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> show #!5.3 models
> close #5
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job020/run_it025_class001.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job020/run_it025_class002.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job020/run_it025_class003.mrc
> /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job020/run_it025_class004.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00706, step 2, values float32
> select #5
9 models selected
> ~select #5
Nothing selected
> hide #!5 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> hide #!5.4 models
> select #5
9 models selected
> ~select #5
Nothing selected
> select #5.1
2 models selected
> ~select #5.1
Nothing selected
> select #5.1
2 models selected
> ~select #5.1
Nothing selected
> volume #5.4 level 0.009539
> volume #5.3 level 0.007131
> volume #5.2 level 0.00451
> show #!5.1 models
> hide #!5 models
> hide #!5.2 models
> hide #!5.1 models
> hide #!5.3 models
> hide #!5.4 models
> volume #5.4 level 0.01099
> volume #5.3 level 0.006065
> show #!5 models
> hide #!5.3 models
> hide #!5.4 models
> show #!5.1 models
> show #!5.2 models
> hide #!5.2 models
> hide #!5.1 models
> show #!5.3 models
> show #!5.4 models
> hide #!5.3 models
> hide #!5.4 models
> show #!5.4 models
> show #!5.3 models
> close session
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job031/run_it021_class001.mrc
Opened run_it021_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00547, step 2, values float32
> volume #1 step 1
> volume #1 level 0.004611
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job031/run_it025_class001.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00542, step 2, values float32
> volume #2 level 0.004385
> volume #2 level 0.004256
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Refine3D/run_ct4_class001.mrc
Opened run_ct4_class001.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.00674, step 2, values float32
> volume #3 level 0.005715
> open /Users/hchou01/temp/MaskCreate/arctica/job075/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> hide #!4 models
> show #!4 models
> volume #4 level 1
> close #4
> open /Users/hchou01/temp/MaskCreate/job039/mask.mrc
Opened mask.mrc, grid size 480,480,480, pixel 0.83, shown at level 0.0952,
step 2, values float32
> volume #4 level 1
> ui tool show "Map Coordinates"
> close #3
> volume #2 level 0.004091
> volume #2 level 0.004091
> close #4
> open /Users/hchou01/temp/MaskCreate/job039/mask.mrc
Opened mask.mrc, grid size 480,480,480, pixel 0.83, shown at level 0.0952,
step 2, values float32
> volume #3 level 0.008665
> volume #3 level 1
> volume #3 step 1
> select #3
2 models selected
> close #3
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job036/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #3 step 1
> volume #3 level 0.8407
> volume #3 level 1
> volume #3 style mesh
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job037/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #4 step 1
> volume #4 style mesh
> volume #4 level 1
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Refine3D/run_ct4_class001.mrc
Opened run_ct4_class001.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.00674, step 2, values float32
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job038/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #6 style mesh
> volume #6 level 1
> close #3
> close #6
> close #4
> close #1
> open /Users/hchou01/temp/LD-
> CAMK2D-CaM/Class3D/job034/run_ct15_it021_class001.mrc
Opened run_ct15_it021_class001.mrc, grid size 320,320,320, pixel 0.83, shown
at level 0.00698, step 2, values float32
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job039/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #3 level 1
> volume #3 style mesh
> volume #5 level 0.008731
> volume #5 level 0.00674
> volume #5 level 0.00873
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job040/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #4 level 1
> volume #4 style mesh
> volume #5 level 0.00647
> volume #5 level 0.00553
> close #4
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job039/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #4 level 1
> volume #4 style mesh
> volume #4 level 1
> close #3
> close #4
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job037/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #3 level 1
> close #3
> open /Users/hchou01/temp/LD-CAMK2D-CaM/MaskCreate/job039/mask.mrc
Opened mask.mrc, grid size 320,320,320, pixel 0.83, shown at level 1, step 2,
values float32
> volume #3 level 1
> volume #3 style mesh
> volume #1 level 0.006324
> volume #5 level 0.007742
> open /Users/hchou01/temp/LD-
> CAMK2D-CaM/Class3D/job034/run_ct15_it021_class001.mrc
Opened run_ct15_it021_class001.mrc, grid size 320,320,320, pixel 0.83, shown
at level 0.00698, step 2, values float32
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job031/run_it025_class001.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00542, step 2, values float32
> close #6
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Class3D/job028/run_it025_class001.mrc
Opened run_it025_class001.mrc, grid size 320,320,320, pixel 0.83, shown at
level 0.00686, step 2, values float32
> open /Users/hchou01/temp/3soa.pdb1
3soa.pdb1 title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb1
---
Chain | Description
7.1/A | No description available
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 7.11/A 7.12/A | No
description available
> select #4
2 models selected
> ui tool show "Fit in Map"
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> open /Users/hchou01/temp/3soa.pdb1
3soa.pdb1 title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb1
---
Chain | Description
1.1/A | No description available
1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A | No
description available
> select #7
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ~select #7
Nothing selected
> close #1
> open /Users/hchou01/temp/LD-CAMK2D-CaM/PostProcess/postprocess.mrc
Opened postprocess.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.0098, step 2, values float32
> volume #1 level 0.01467
> select #7
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #1 step 1
Fit molecules 3soa.pdb1 (#7.1), 3soa.pdb1 (#7.2), 3soa.pdb1 (#7.3), 3soa.pdb1
(#7.4), 3soa.pdb1 (#7.5), 3soa.pdb1 (#7.6), 3soa.pdb1 (#7.7), 3soa.pdb1
(#7.8), 3soa.pdb1 (#7.9), 3soa.pdb1 (#7.10), 3soa.pdb1 (#7.11), 3soa.pdb1
(#7.12) to map postprocess.mrc (#1) using 42492 atoms
average map value = 0.004408, steps = 148
shifted from previous position = 4.49
rotated from previous position = 9.66 degrees
atoms outside contour = 38487, contour level = 0.014669
Position of 3soa.pdb1 (#7.1) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.4) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.6) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.7) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.8) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.9) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.10) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.11) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Position of 3soa.pdb1 (#7.12) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98877191 -0.14925338 0.00731658 23.20158858
0.14824485 0.98589729 0.07765301 -24.06715026
-0.01880337 -0.07569647 0.99695360 14.22524330
Axis -0.45678682 0.07780433 0.88616719
Axis point 175.98641967 142.62572727 -0.00000000
Rotation angle (degrees) 9.66322740
Shift along axis 0.13523543
Fit molecules 3soa.pdb1 (#7.1), 3soa.pdb1 (#7.2), 3soa.pdb1 (#7.3), 3soa.pdb1
(#7.4), 3soa.pdb1 (#7.5), 3soa.pdb1 (#7.6), 3soa.pdb1 (#7.7), 3soa.pdb1
(#7.8), 3soa.pdb1 (#7.9), 3soa.pdb1 (#7.10), 3soa.pdb1 (#7.11), 3soa.pdb1
(#7.12) to map postprocess.mrc (#1) using 42492 atoms
average map value = 0.01046, steps = 56
shifted from previous position = 2.62
rotated from previous position = 1.42 degrees
atoms outside contour = 32303, contour level = 0.014669
Position of 3soa.pdb1 (#7.1) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.4) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.6) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.7) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.8) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.9) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.10) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.11) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
Position of 3soa.pdb1 (#7.12) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.98870846 -0.14970051 -0.00673376 24.85483928
0.14963581 0.98387330 0.09799210 -24.81347540
-0.00804430 -0.09789323 0.99516441 17.75963987
Axis -0.54756959 0.00366342 0.83675213
Axis point 182.71962403 156.49046553 0.00000000
Rotation angle (degrees) 10.30382949
Shift along axis 1.15976018
> ~select #7
Nothing selected
> select #7
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ~select #7
Nothing selected
> hide #!7 models
> volume #1 level 0.01322
> volume #1 level 0.01226
> close session
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Refine3D/run_ct4_class001.mrc
Opened run_ct4_class001.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.00674, step 2, values float32
> volume #1 level 0.00987
> volume #1 level 0.008359
> volume #1 level 0.007604
> volume #1 level 0.006254
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/3soa.pdb1
3soa.pdb1 title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb1
---
Chain | Description
2.1/A | No description available
2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A | No
description available
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel.pdb
Summary of feedback from opening
/Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA 5 TYR A
6 GLY A 15 0
Start residue of secondary structure not found: SHEET 2 AA 5 SER A 18 LYS A 25
-1
Start residue of secondary structure not found: SHEET 3 AA 5 GLU A 31 ASN A 38
-1
Start residue of secondary structure not found: SHEET 4 AA 5 PHE A 77 PHE A 82
-1
Start residue of secondary structure not found: SHEET 5 AA 5 LEU A 68 GLU A 74
-1
6 messages similar to the above omitted
> select #3
1235 atoms, 991 bonds, 257 residues, 1 model selected
> select #2
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> rainbow sel
> rainbow sel
> rainbow sel
> select #3
1235 atoms, 991 bonds, 257 residues, 1 model selected
> color sel bychain
> color sel bychain
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> select #2
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> show sel cartoons
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> select
> #2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A#2.11/A#2.12/A
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 24 models selected
> color (#!2.1-12 & sel) orange
> select #3
1235 atoms, 991 bonds, 257 residues, 1 model selected
> color sel forest green
> rainbow sel
> rainbow sel
> rainbow sel
> show sel cartoons
> show sel surfaces
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> cartoon (#!3 & sel)
> hide sel surfaces
> show sel cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
> close #3.1
> rainbow sel
> rainbow sel
> rainbow sel
> rainbow sel
> close #3
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel.pdb
Summary of feedback from opening
/Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA 5 TYR A
6 GLY A 15 0
Start residue of secondary structure not found: SHEET 2 AA 5 SER A 18 LYS A 25
-1
Start residue of secondary structure not found: SHEET 3 AA 5 GLU A 31 ASN A 38
-1
Start residue of secondary structure not found: SHEET 4 AA 5 PHE A 77 PHE A 82
-1
Start residue of secondary structure not found: SHEET 5 AA 5 LEU A 68 GLU A 74
-1
6 messages similar to the above omitted
> select #3
1235 atoms, 991 bonds, 257 residues, 1 model selected
> rainbow sel
> rainbow sel
> style sel sphere
Changed 1235 atom styles
> style sel sphere
Changed 1235 atom styles
> nucleotides sel ladder
> nucleotides sel ladder
> style sel ball
Changed 1235 atom styles
> style sel sphere
Changed 1235 atom styles
> style sel stick
Changed 1235 atom styles
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> close #2
> close
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel.pdb format pdb
Summary of feedback from opening
/Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA 5 TYR A
6 GLY A 15 0
Start residue of secondary structure not found: SHEET 2 AA 5 SER A 18 LYS A 25
-1
Start residue of secondary structure not found: SHEET 3 AA 5 GLU A 31 ASN A 38
-1
Start residue of secondary structure not found: SHEET 4 AA 5 PHE A 77 PHE A 82
-1
Start residue of secondary structure not found: SHEET 5 AA 5 LEU A 68 GLU A 74
-1
6 messages similar to the above omitted
> rainbow
> rainbow
> rainbow
> select #1
1235 atoms, 991 bonds, 257 residues, 1 model selected
> ui tool show "Model Panel"
> ~select #1
Nothing selected
> select #1
1235 atoms, 991 bonds, 257 residues, 1 model selected
> color sel bychain
> color sel bychain
> color sel byhetero
> rainbow sel
> color sel byhetero
> mlp sel
mlp: no amino acids specified
> coulombic sel
Don't know how to assign charges to the following residue types: CA
> coulombic sel
Don't know how to assign charges to the following residue types: CA
> color sel bychain
> mlp sel
mlp: no amino acids specified
> color bfactor sel
1235 atoms, 257 residues, atom bfactor range 4.35 to 85.2
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> coulombic sel
Don't know how to assign charges to the following residue types: CA
> coulombic sel
Don't know how to assign charges to the following residue types: CA
> coulombic sel
Don't know how to assign charges to the following residue types: CA
> color bfactor sel
1235 atoms, 257 residues, atom bfactor range 4.35 to 85.2
> hbonds sel
491 hydrogen bonds found
> hbonds sel
491 hydrogen bonds found
> ~hbonds
> interfaces sel & ~solvent
0 buried areas:
> nucleotides sel ladder
> rainbow sel
> rainbow sel
> close session
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Refine3D/job029/run_ct4_class001.mrc
Opened run_ct4_class001.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.00674, step 2, values float32
> open /Users/hchou01/temp/LD-CAMK2D-CaM/Refine3D/job043/run_ct5_class001.mrc
Opened run_ct5_class001.mrc, grid size 320,320,320, pixel 0.83, shown at level
0.00683, step 2, values float32
> volume #2 step 1
> volume #2 level 0.008089
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/2wel.pdb
2wel.pdb title:
Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase
II δ In complex with calmodulin [more info...]
Chain information for 2wel.pdb #3
---
Chain | Description
A | calcium/calmodulin-dependent protein kinase type II δ chain
D | CAM
Non-standard residues in 2wel.pdb #3
---
CA — calcium ion
EDO — 1,2-ethanediol (ethylene glycol)
K88 —
(3Z)-N,N-dimethyl-2-oxo-3-(4,5,6,7-tetrahydro-1H-indol-2-ylmethylidene)-2,3-dihydro-1H-indole-5-sulfonamide
PO4 — phosphate ion
> select #3
4013 atoms, 3666 bonds, 30 pseudobonds, 867 residues, 3 models selected
> volume #1 level 0.009493
> volume #1 level 0.009493
> volume #2 level 0.01091
> volume #1 level 0.008521
> volume #1 step 1
> close #1
> volume #2 level 0.01001
> volume #2 level 0.007969
> select /A
2778 atoms, 2531 bonds, 2 pseudobonds, 610 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select /D
1235 atoms, 1135 bonds, 28 pseudobonds, 257 residues, 2 models selected
> save /Users/hchou01/Documents/Projects/CAMK2D/pdb/CaM_2wel-2.pdb
> selectedOnly true relModel #3
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
opened ChimeraX session
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/3soa.pdb
3soa.pdb title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb #1
---
Chain | Description
A | calcium/calmodulin-dependent protein kinase type II subunit α with A β 7
linker
Non-standard residues in 3soa.pdb #1
---
DB8 —
4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
(bosutinib)
> ~select #3
Nothing selected
> select #1
3541 atoms, 3629 bonds, 2 pseudobonds, 437 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
Fit molecule 3soa.pdb (#1) to map run_ct5_class001.mrc (#2) using 3541 atoms
average map value = 0.007311, steps = 192
shifted from previous position = 15.6
rotated from previous position = 21.3 degrees
atoms outside contour = 2063, contour level = 0.0079694
Position of 3soa.pdb (#1) relative to run_ct5_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.94091210 -0.05331374 0.33442798 118.16819122
-0.33864673 0.15302729 -0.92838626 163.68361061
-0.00168086 -0.98678280 -0.16203975 114.08034318
Axis -0.13130472 0.75574127 -0.64157167
Axis point 83.47424095 0.00000000 117.37316685
Rotation angle (degrees) 167.15170878
Shift along axis 34.99570295
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/3soa.pdb1
3soa.pdb1 title:
Full-length human camkii [more info...]
Chain information for 3soa.pdb1
---
Chain | Description
4.1/A | No description available
4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A | No
description available
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ui mousemode right "rotate selected models"
> select
> #4.1/A#4.2/A#4.3/A#4.4/A#4.5/A#4.6/A#4.7/A#4.8/A#4.9/A#4.10/A#4.11/A#4.12/A
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 24 models selected
Fit molecules 3soa.pdb1 (#4.1), 3soa.pdb1 (#4.2), 3soa.pdb1 (#4.3), 3soa.pdb1
(#4.4), 3soa.pdb1 (#4.5), 3soa.pdb1 (#4.6), 3soa.pdb1 (#4.7), 3soa.pdb1
(#4.8), 3soa.pdb1 (#4.9), 3soa.pdb1 (#4.10), 3soa.pdb1 (#4.11), 3soa.pdb1
(#4.12) to map run_ct5_class001.mrc (#2) using 42492 atoms
average map value = 0.005981, steps = 144
shifted from previous position = 10.5
rotated from previous position = 9.29 degrees
atoms outside contour = 30711, contour level = 0.0079694
Position of 3soa.pdb1 (#4.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
Position of 3soa.pdb1 (#4.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98794682 0.08277413 0.13080342 -23.23265266
-0.08869721 0.99525053 0.04011460 10.54827223
-0.12686172 -0.05123299 0.99059643 34.17249055
Axis -0.28306895 0.79845562 -0.53135731
Axis point 240.81921890 0.00000000 206.64227303
Rotation angle (degrees) 9.28539120
Shift along axis -3.15903287
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/camk2a-hub.pdb
Summary of feedback from opening
/Users/hchou01/Documents/Projects/CAMK2D/pdb/camk2a-hub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 7
GLU A 12 1 6
Start residue of secondary structure not found: HELIX 2 2 LEU A 49 LEU A 67 1
19
Start residue of secondary structure not found: HELIX 3 3 GLU A 96 ARG A 104 1
9
Start residue of secondary structure not found: HELIX 4 4 SER A 108 MET A 129
1 22
Start residue of secondary structure not found: HELIX 5 5 THR A 176 LEU A 180
1 5
15 messages similar to the above omitted
camk2a-hub.pdb title:
Full-length human camkii [more info...]
Chain information for camk2a-hub.pdb
---
Chain | Description
5.1/A | No description available
5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A | No
description available
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
run_ct5_class001.mrc (#2) using 12852 atoms
average map value = 0.005779, steps = 100
shifted from previous position = 3.27
rotated from previous position = 7.79 degrees
atoms outside contour = 9417, contour level = 0.0079694
Position of camk2a-hub.pdb (#5.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
Position of camk2a-hub.pdb (#5.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99129238 -0.07454206 -0.10854909 25.88797092
0.07103095 0.99682908 -0.03586628 -4.36726275
0.11087844 0.02784362 0.99344386 -13.65942831
Axis 0.23515930 -0.80992791 0.53732382
Axis point 147.37809722 0.00000000 221.71735433
Rotation angle (degrees) 7.78528687
Shift along axis 2.28542888
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
run_ct5_class001.mrc (#2) using 12852 atoms
average map value = 0.005876, steps = 84
shifted from previous position = 6.51
rotated from previous position = 2.55 degrees
atoms outside contour = 9294, contour level = 0.0079694
Position of camk2a-hub.pdb (#5.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
Position of camk2a-hub.pdb (#5.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.98543466 -0.10677659 -0.13235288 31.25438045
0.10483535 0.99425564 -0.02156996 -6.89881463
0.13389576 0.00738053 0.99096794 -8.52035650
Axis 0.08481676 -0.78003322 0.61996313
Axis point 91.49801095 0.00000000 224.31279334
Rotation angle (degrees) 9.82648221
Shift along axis 2.74989308
> ui mousemode right "rotate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
run_ct5_class001.mrc (#2) using 12852 atoms
average map value = 0.01288, steps = 96
shifted from previous position = 7.46
rotated from previous position = 7.94 degrees
atoms outside contour = 3018, contour level = 0.0079694
Position of camk2a-hub.pdb (#5.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
Position of camk2a-hub.pdb (#5.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.96077791 -0.10724400 -0.25574311 53.64025972
0.09019285 0.99290207 -0.07752891 -3.61758575
0.26224237 0.05142186 0.96363101 -25.08264507
Axis 0.22657189 -0.91012211 0.34690479
Axis point 130.06182891 0.00000000 183.82056261
Rotation angle (degrees) 16.53310058
Shift along axis 6.74452996
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
run_ct5_class001.mrc (#2) using 12852 atoms
average map value = 0.01288, steps = 132
shifted from previous position = 3.25
rotated from previous position = 14.7 degrees
atoms outside contour = 3016, contour level = 0.0079694
Position of camk2a-hub.pdb (#5.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
Position of camk2a-hub.pdb (#5.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.90080187 -0.11223089 -0.41947612 83.39315720
0.00724044 0.96976993 -0.24391362 27.94887059
0.43416997 0.21668066 0.87438317 -60.13894026
Axis 0.47128847 -0.87346624 0.12224524
Axis point 183.17306412 0.00000000 147.01693772
Rotation angle (degrees) 29.25217141
Shift along axis 7.53813953
> ui mousemode right "translate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
run_ct5_class001.mrc (#2) using 12852 atoms
average map value = 0.01288, steps = 216
shifted from previous position = 11.1
rotated from previous position = 29.3 degrees
atoms outside contour = 3017, contour level = 0.0079694
Position of camk2a-hub.pdb (#5.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
Position of camk2a-hub.pdb (#5.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.69819890 -0.17546165 -0.69406880 161.31260462
-0.25890834 0.84199070 -0.47330553 103.76924023
0.66744645 0.51016160 0.54244850 -94.33896231
Axis 0.58482810 -0.80963801 -0.04962237
Axis point 224.08880855 0.00000000 122.33147062
Rotation angle (degrees) 57.22652241
Shift along axis 15.00594513
> open /Users/hchou01/temp/LD-
> CAMK2D-CaM/Class3D/job016/hubs_align2_arctica_job058.mrc
Opened hubs_align2_arctica_job058.mrc, grid size 320,320,320, pixel 0.83,
shown at level 0.0049, step 2, values float32
> hide #!2 models
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 228
shifted from previous position = 11.5
rotated from previous position = 31.5 degrees
atoms outside contour = 1360, contour level = 0.0048984
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.68046508 -0.18122586 -0.71001723 166.69053688
-0.28503134 0.82717229 -0.48429654 110.77396864
0.67507363 0.53192404 0.51120681 -95.02862616
Axis 0.59047110 -0.80480177 -0.06031578
Axis point 226.55426469 0.00000000 120.33170587
Rotation angle (degrees) 59.37465687
Shift along axis 15.00658350
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #6 level 0.006705
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 144
shifted from previous position = 5.41
rotated from previous position = 16.5 degrees
atoms outside contour = 2785, contour level = 0.0067051
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.81656107 0.03796569 -0.57600923 93.62152925
-0.05675087 0.99828084 -0.01465277 9.29015761
0.57446267 0.04465391 0.81731185 -49.26209926
Axis 0.05130839 -0.99531544 -0.08194278
Axis point 124.86544937 0.00000000 122.80566513
Rotation angle (degrees) 35.30601894
Shift along axis -0.40639438
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 96
shifted from previous position = 1.77
rotated from previous position = 7.01 degrees
atoms outside contour = 2781, contour level = 0.0067051
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76577205 0.06640003 -0.63967507 104.49040641
-0.02674371 0.99708313 0.07148437 -5.33121778
0.64255579 -0.03763345 0.76531417 -38.96660768
Axis -0.08457225 -0.99379874 -0.07219147
Axis point 106.15413001 0.00000000 124.38308953
Rotation angle (degrees) 40.17437067
Shift along axis -0.72577426
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 56
shifted from previous position = 2.49
rotated from previous position = 0.208 degrees
atoms outside contour = 2785, contour level = 0.0067051
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.76403135 0.06665565 -0.64172667 104.34650103
-0.02843076 0.99716103 0.06972505 -3.73914402
0.64455239 -0.03502735 0.76375736 -41.50301559
Axis -0.08095016 -0.99400588 -0.07348051
Axis point 109.36262743 0.00000000 122.17711878
Rotation angle (degrees) 40.31713476
Shift along axis -1.68047193
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 68
shifted from previous position = 3.21
rotated from previous position = 3.18 degrees
atoms outside contour = 2783, contour level = 0.0067051
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671499 0.11374197 -0.61949704 91.17093773
-0.07476501 0.99325505 0.08862621 -0.02386488
0.62539908 -0.02252061 0.77998001 -44.55194620
Axis -0.08793374 -0.98489886 -0.14913719
Axis point 109.39565753 0.00000000 107.54836189
Rotation angle (degrees) 39.19723196
Shift along axis -1.34914536
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 84
shifted from previous position = 3.7
rotated from previous position = 3.18 degrees
atoms outside contour = 2785, contour level = 0.0067051
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77671209 0.11373135 -0.61950263 91.44977462
-0.07475831 0.99325634 0.08861739 2.43190095
0.62540349 -0.02251723 0.77997657 -44.83536617
Axis -0.08792366 -0.98490194 -0.14912276
Axis point 110.33934995 0.00000000 107.31614555
Rotation angle (degrees) 39.19746083
Shift along axis -3.74980947
Average map value = 0.006837 for 12852 atoms, 7075 outside contour
> ui mousemode right "rotate selected models"
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 2784, contour level = 0.0067051
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
> ui tool show "Segment Map"
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
> ~select #5
Nothing selected
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
Fit molecules 3soa.pdb1 (#4.1), 3soa.pdb1 (#4.2), 3soa.pdb1 (#4.3), 3soa.pdb1
(#4.4), 3soa.pdb1 (#4.5), 3soa.pdb1 (#4.6), 3soa.pdb1 (#4.7), 3soa.pdb1
(#4.8), 3soa.pdb1 (#4.9), 3soa.pdb1 (#4.10), 3soa.pdb1 (#4.11), 3soa.pdb1
(#4.12) to map hubs_align2_arctica_job058.mrc (#6) using 42492 atoms
average map value = 0.005265, steps = 892
shifted from previous position = 144
rotated from previous position = 5.21 degrees
atoms outside contour = 32183, contour level = 0.0067051
Position of 3soa.pdb1 (#4.1) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.2) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.3) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.4) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.5) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.6) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.7) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.8) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.9) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.10) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.11) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Position of 3soa.pdb1 (#4.12) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98445214 0.08297361 0.15482041 16.15415534
-0.07734554 0.99611766 -0.04203897 157.20013580
-0.15770747 0.02941069 0.98704780 17.15079880
Axis 0.19933372 0.87190542 -0.44726614
Axis point 475.47214698 0.00000000 114.14909974
Rotation angle (degrees) 10.32440035
Shift along axis 132.61274750
Fit molecules 3soa.pdb1 (#4.1), 3soa.pdb1 (#4.2), 3soa.pdb1 (#4.3), 3soa.pdb1
(#4.4), 3soa.pdb1 (#4.5), 3soa.pdb1 (#4.6), 3soa.pdb1 (#4.7), 3soa.pdb1
(#4.8), 3soa.pdb1 (#4.9), 3soa.pdb1 (#4.10), 3soa.pdb1 (#4.11), 3soa.pdb1
(#4.12) to map hubs_align2_arctica_job058.mrc (#6) using 42492 atoms
average map value = 0.005265, steps = 600
shifted from previous position = 87.1
rotated from previous position = 2.99 degrees
atoms outside contour = 32181, contour level = 0.0067051
Position of 3soa.pdb1 (#4.1) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.2) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.3) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.4) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.5) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.6) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.7) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.8) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.9) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.10) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.11) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
Position of 3soa.pdb1 (#4.12) relative to hubs_align2_arctica_job058.mrc (#6)
coordinates:
Matrix rotation and translation
0.98947920 0.09246207 0.11127301 108.06909558
-0.08500597 0.99391909 -0.06999161 151.44225144
-0.11706794 0.05979637 0.99132209 13.65512620
Axis 0.40944532 0.72035281 -0.55986280
Axis point 839.77900300 0.00000000 -355.69912769
Rotation angle (degrees) 9.11940268
Shift along axis 145.69524049
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected atoms"
> volume #6 style mesh
> ~select #4
Nothing selected
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
> ui tool show "Fit in Map"
> save /Users/hchou01/Documents/Projects/CAMK2D/pdb/camk2a-hub_align.pdb
> models #5 selectedOnly true relModel #6
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/camk2a-hub_align.pdb
camk2a-hub_align.pdb title:
Full-length human camkii [more info...]
Chain information for camk2a-hub_align.pdb
---
Chain | Description
7.1/A | No description available
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 7.11/A 7.12/A | No
description available
> select #7
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
Fit molecules camk2a-hub_align.pdb (#7.1), camk2a-hub_align.pdb (#7.2),
camk2a-hub_align.pdb (#7.3), camk2a-hub_align.pdb (#7.4), camk2a-hub_align.pdb
(#7.5), camk2a-hub_align.pdb (#7.6), camk2a-hub_align.pdb (#7.7),
camk2a-hub_align.pdb (#7.8), camk2a-hub_align.pdb (#7.9), camk2a-hub_align.pdb
(#7.10), camk2a-hub_align.pdb (#7.11), camk2a-hub_align.pdb (#7.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 2784, contour level = 0.0067051
Position of camk2a-hub_align.pdb (#7.1) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.2) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.3) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.4) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.5) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.6) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.7) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.8) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.9) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.10) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.11) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.12) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
> volume #6 style surface
> hide #!5 models
> volume #6 level 0.01175
> select #6
2 models selected
> ~select #6
Nothing selected
> select #6
2 models selected
> ~select #6
Nothing selected
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> select #7
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> ~select #5
Nothing selected
> select #7
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> show #!5 models
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 7678, contour level = 0.011746
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 7678, contour level = 0.011746
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
> select #7
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
Fit molecules camk2a-hub_align.pdb (#7.1), camk2a-hub_align.pdb (#7.2),
camk2a-hub_align.pdb (#7.3), camk2a-hub_align.pdb (#7.4), camk2a-hub_align.pdb
(#7.5), camk2a-hub_align.pdb (#7.6), camk2a-hub_align.pdb (#7.7),
camk2a-hub_align.pdb (#7.8), camk2a-hub_align.pdb (#7.9), camk2a-hub_align.pdb
(#7.10), camk2a-hub_align.pdb (#7.11), camk2a-hub_align.pdb (#7.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 7678, contour level = 0.011746
Position of camk2a-hub_align.pdb (#7.1) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.2) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.3) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.4) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.5) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.6) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.7) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.8) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.9) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.10) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.11) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.12) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
Fit molecules camk2a-hub_align.pdb (#7.1), camk2a-hub_align.pdb (#7.2),
camk2a-hub_align.pdb (#7.3), camk2a-hub_align.pdb (#7.4), camk2a-hub_align.pdb
(#7.5), camk2a-hub_align.pdb (#7.6), camk2a-hub_align.pdb (#7.7),
camk2a-hub_align.pdb (#7.8), camk2a-hub_align.pdb (#7.9), camk2a-hub_align.pdb
(#7.10), camk2a-hub_align.pdb (#7.11), camk2a-hub_align.pdb (#7.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 7678, contour level = 0.011746
Position of camk2a-hub_align.pdb (#7.1) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.2) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.3) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.4) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.5) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.6) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.7) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.8) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.9) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.10) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.11) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Position of camk2a-hub_align.pdb (#7.12) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99942061 0.02408093 0.02405321 -6.90162338
-0.02410157 0.99970935 0.00056845 3.25150388
-0.02403253 -0.00114784 0.99971052 2.04386270
Axis -0.02520495 0.70617125 -0.70759231
Axis point 101.43701868 287.97012504 0.00000000
Rotation angle (degrees) 1.95111480
Shift along axis 1.02385205
Fit molecules camk2a-hub_align.pdb (#7.1), camk2a-hub_align.pdb (#7.2),
camk2a-hub_align.pdb (#7.3), camk2a-hub_align.pdb (#7.4), camk2a-hub_align.pdb
(#7.5), camk2a-hub_align.pdb (#7.6), camk2a-hub_align.pdb (#7.7),
camk2a-hub_align.pdb (#7.8), camk2a-hub_align.pdb (#7.9), camk2a-hub_align.pdb
(#7.10), camk2a-hub_align.pdb (#7.11), camk2a-hub_align.pdb (#7.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 40
shifted from previous position = 0.0139
rotated from previous position = 0.0177 degrees
atoms outside contour = 7689, contour level = 0.011746
Position of camk2a-hub_align.pdb (#7.1) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.2) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.3) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.4) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.5) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.6) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.7) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.8) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.9) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.10) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.11) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
Position of camk2a-hub_align.pdb (#7.12) relative to
hubs_align2_arctica_job058.mrc (#6) coordinates:
Matrix rotation and translation
0.99941336 0.02438955 0.02404352 -6.94039902
-0.02440991 0.99970188 0.00055353 3.29581216
-0.02402285 -0.00114010 0.99971076 2.05545789
Axis -0.02471829 0.70152081 -0.71222016
Axis point 102.22137252 285.98973888 0.00000000
Rotation angle (degrees) 1.96326251
Shift along axis 1.01969706
> select #5
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
Fit molecules camk2a-hub.pdb (#5.1), camk2a-hub.pdb (#5.2), camk2a-hub.pdb
(#5.3), camk2a-hub.pdb (#5.4), camk2a-hub.pdb (#5.5), camk2a-hub.pdb (#5.6),
camk2a-hub.pdb (#5.7), camk2a-hub.pdb (#5.8), camk2a-hub.pdb (#5.9),
camk2a-hub.pdb (#5.10), camk2a-hub.pdb (#5.11), camk2a-hub.pdb (#5.12) to map
hubs_align2_arctica_job058.mrc (#6) using 12852 atoms
average map value = 0.01164, steps = 52
shifted from previous position = 1.47
rotated from previous position = 1.95 degrees
atoms outside contour = 7678, contour level = 0.011746
Position of camk2a-hub.pdb (#5.1) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.2) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.3) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.4) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.5) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.6) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.7) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.8) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.9) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.10) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.11) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
Position of camk2a-hub.pdb (#5.12) relative to hubs_align2_arctica_job058.mrc
(#6) coordinates:
Matrix rotation and translation
0.77840736 0.08978751 -0.62130522 96.29608319
-0.04647072 0.99524474 0.08560590 -3.02508670
0.62603710 -0.03776377 0.77887833 -41.95055580
Axis -0.09784931 -0.98931593 -0.10807172
Axis point 108.32870822 0.00000000 116.05521340
Rotation angle (degrees) 39.08011712
Shift along axis -1.89606948
> close #5
> select #7
12852 atoms, 13200 bonds, 1584 residues, 13 models selected
> show #!2 models
> hide #!2 models
Fit map hubs_align2_arctica_job058.mrc in map run_ct5_class001.mrc using 9837
points
correlation = 0.9887, correlation about mean = 0.6911, overlap = 2.55
steps = 72, shift = 0.692, angle = 2.24 degrees
Position of hubs_align2_arctica_job058.mrc (#6) relative to
run_ct5_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.99970808 -0.00855168 0.02259704 -2.09582312
0.00785468 0.99949606 0.03075586 -5.23152888
-0.02284867 -0.03056939 0.99927146 7.81492289
Axis -0.78549413 0.58209853 0.21014349
Axis point 0.00000000 249.71215437 178.79395021
Rotation angle (degrees) 2.23717189
Shift along axis 0.24324664
> show #!2 models
> volume #2 level 0.01399
Fit map hubs_align2_arctica_job058.mrc in map run_ct5_class001.mrc using 9837
points
correlation = 0.9887, correlation about mean = 0.6911, overlap = 2.55
steps = 72, shift = 0.692, angle = 2.24 degrees
Position of hubs_align2_arctica_job058.mrc (#6) relative to
run_ct5_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.99970808 -0.00855168 0.02259704 -2.09582312
0.00785468 0.99949606 0.03075586 -5.23152888
-0.02284867 -0.03056939 0.99927146 7.81492289
Axis -0.78549413 0.58209853 0.21014349
Axis point 0.00000000 249.71215437 178.79395021
Rotation angle (degrees) 2.23717189
Shift along axis 0.24324664
Fit molecules camk2a-hub_align.pdb (#7.1), camk2a-hub_align.pdb (#7.2),
camk2a-hub_align.pdb (#7.3), camk2a-hub_align.pdb (#7.4), camk2a-hub_align.pdb
(#7.5), camk2a-hub_align.pdb (#7.6), camk2a-hub_align.pdb (#7.7),
camk2a-hub_align.pdb (#7.8), camk2a-hub_align.pdb (#7.9), camk2a-hub_align.pdb
(#7.10), camk2a-hub_align.pdb (#7.11), camk2a-hub_align.pdb (#7.12) to map
run_ct5_class001.mrc (#2) using 12852 atoms
average map value = 0.01288, steps = 60
shifted from previous position = 0.673
rotated from previous position = 2.27 degrees
atoms outside contour = 7221, contour level = 0.013992
Position of camk2a-hub_align.pdb (#7.1) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.2) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.3) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.4) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.5) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.6) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.7) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.8) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.9) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.10) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.11) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
Position of camk2a-hub_align.pdb (#7.12) relative to run_ct5_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99875825 0.01584491 0.04723244 -9.09054510
-0.01736124 0.99934129 0.03186816 -1.95027932
-0.04669638 -0.03264860 0.99837544 10.05084246
Axis -0.54356661 0.79136902 -0.27976852
Axis point 212.09396985 0.00000000 191.29596129
Rotation angle (degrees) 3.40226138
Shift along axis 0.58601686
> save /Users/hchou01/Documents/Projects/CAMK2D/pdb/camk2a-hub_align_2.pdb
> models #7 selectedOnly true relModel #2
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
> open /Users/hchou01/Documents/Projects/CAMK2D/pdb/camk2a-hub_align_2.pdb
camk2a-hub_align_2.pdb title:
Full-length human camkii [more info...]
Chain information for camk2a-hub_align_2.pdb
---
Chain | Description
5.1/A | No description available
5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A | No
description available
> hide #!7 models
> show #!7 models
> close #7
> save
> /Users/hchou01/Documents/Projects/CAMK2D/pdb/ChimeraX/session_20210627.cxs
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ~select #4
Nothing selected
> select #4
42492 atoms, 43548 bonds, 24 pseudobonds, 5244 residues, 25 models selected
> ui mousemode right "rotate selected models"
> toolshed show
> ui tool show Matchmaker
> matchmaker
> #5.1/A#5.2/A#5.3/A#5.4/A#5.5/A#5.6/A#5.7/A#5.8/A#5.9/A#5.10/A#5.11/A#5.12/A
> to
> #4.1/A#4.2/A#4.3/A#4.4/A#4.5/A#4.6/A#4.7/A#4.8/A#4.9/A#4.10/A#4.11/A#4.12/A
> pairing ss
Parameters
---
Chain pairing | ss
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 3soa.pdb1, chain A (#4.1) with camk2a-hub_align_2.pdb, chain A
(#5.1), sequence alignment score = 1864.7
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.2) with camk2a-hub_align_2.pdb, chain A
(#5.2), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.3) with camk2a-hub_align_2.pdb, chain A
(#5.3), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.4) with camk2a-hub_align_2.pdb, chain A
(#5.4), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.5) with camk2a-hub_align_2.pdb, chain A
(#5.5), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.6) with camk2a-hub_align_2.pdb, chain A
(#5.6), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.7) with camk2a-hub_align_2.pdb, chain A
(#5.7), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.8) with camk2a-hub_align_2.pdb, chain A
(#5.8), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.9) with camk2a-hub_align_2.pdb, chain A
(#5.9), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.10) with camk2a-hub_align_2.pdb, chain A
(#5.10), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.11) with camk2a-hub_align_2.pdb, chain A
(#5.11), sequence alignment score = 709.6
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Matchmaker 3soa.pdb1, chain A (#4.12) with camk2a-hub_align_2.pdb, chain A
(#5.12), sequence alignment score = 713.2
RMSD between 132 pruned atom pairs is 0.001 angstroms; (across all 132 pairs:
0.001)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H524)
Kernel Version: Darwin 19.6.0
Time since boot: 1 day 23:05
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
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: 0.29.20
decorator: 4.4.2
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: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
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: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Hui-Ting,
--Eric