![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#3995 closed defect (nonchimerax)
MemoryError writing compressed session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202011201839 (2020-11-20 18:39:56 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/all_states-session-2.cxs"
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1.1, grid size
512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32
Opened 70S_tRNA_head.mrc as #1.3, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_body.mrc as #1.4, grid size 512,512,512, pixel 0.652, shown at
level 2, step 1, values float32
Opened 70S_tRNA_LSU.mrc as #1.5, grid size 512,512,512, pixel 0.652, shown at
level 2, step 1, values float32
Opened 70S_tRNA_atRNA.mrc as #1.6, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened 70S_tRNA_ptRNA.mrc as #1.7, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened 70S_tRNA_apra.mrc as #1.8, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Opened 70S_tRNA_mRNA.mrc as #1.9, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened h1_j620_3d288_6A_sharpened_b50.mrc as #2.1, grid size 288,288,288,
pixel 1.16, shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_head.mrc as #2.3, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_body.mrc as #2.4, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_LSU.mrc as #2.5, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_atrna.mrc as #2.6, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_ptrna.mrc as #2.7, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_apra.mrc as #2.8, grid size 288,288,288, pixel 1.16,
shown at level 2.5, step 1, values float32
Opened 70S_hybridtRNA_1_mRNA.mrc as #2.9, grid size 288,288,288, pixel 1.16,
shown at level 3, step 1, values float32
Opened h2_j621_3d288_95A_sharpened.mrc as #3.1, grid size 288,288,288, pixel
1.16, shown at level 3, step 1, values float32
Opened 70S_hybridtRNA_2_head.mrc as #3.3, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_2_body.mrc as #3.4, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_2_LSU.mrc as #3.5, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_2_atrna.mrc as #3.6, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_2_ptrna.mrc as #3.7, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_2_apra.mrc as #3.8, grid size 288,288,288, pixel 1.16,
shown at level 2.5, step 1, values float32
Opened 70S_hybridtRNA_2_mRNA.mrc as #3.9, grid size 288,288,288, pixel 1.16,
shown at level 3, step 1, values float32
Opened pre1_GDP-Pi_head.mrc as #4.1, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_body.mrc as #4.2, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_LSU.mrc as #4.3, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_atrna.mrc as #4.4, grid size 512,512,512, pixel 0.652,
shown at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_ptrna.mrc as #4.5, grid size 512,512,512, pixel 0.652,
shown at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_EFG.mrc as #4.6, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_apra.mrc as #4.7, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened pre1_GDP-Pi_mrna.mrc as #4.8, grid size 512,512,512, pixel 0.652, shown
at level 3, step 1, values float32
Opened pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc as #4.9, grid size
512,512,512, pixel 0.652, shown at level 4.33, step 1, values float32
Log from Mon Nov 30 18:33:50 2020UCSF ChimeraX version: 1.2.dev202011201839
(2020-11-20)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/all_states-session.cxs"
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1.1, grid size
512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32
Opened 70S_tRNA_head.mrc as #1.3, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_body.mrc as #1.4, grid size 512,512,512, pixel 0.652, shown at
level 2, step 1, values float32
Opened 70S_tRNA_LSU.mrc as #1.5, grid size 512,512,512, pixel 0.652, shown at
level 2, step 1, values float32
Opened 70S_tRNA_atRNA.mrc as #1.6, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened 70S_tRNA_ptRNA.mrc as #1.7, grid size 512,512,512, pixel 0.652, shown
at level 2.5, step 1, values float32
Opened 70S_tRNA_apra.mrc as #1.8, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Opened 70S_tRNA_mRNA.mrc as #1.9, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened h1_j620_3d288_6A_sharpened_b50.mrc as #2.1, grid size 288,288,288,
pixel 1.16, shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_head.mrc as #2.3, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_body.mrc as #2.4, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_LSU.mrc as #2.5, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_atrna.mrc as #2.6, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_ptrna.mrc as #2.7, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_apra.mrc as #2.8, grid size 288,288,288, pixel 1.16,
shown at level 2.5, step 1, values float32
Opened 70S_hybridtRNA_1_mRNA.mrc as #2.9, grid size 288,288,288, pixel 1.16,
shown at level 3, step 1, values float32
Opened h2_j621_3d288_95A_sharpened.mrc as #3.1, grid size 288,288,288, pixel
1.16, shown at level 3, step 1, values float32
Opened 70S_hybridtRNA_2_head.mrc as #3.3, grid size 288,288,288, pixel 1.16,
shown at level 2, step 2, values float32
Opened 70S_hybridtRNA_2_body.mrc as #3.4, grid size 288,288,288, pixel 1.16,
shown at level 2, step 2, values float32
Opened 70S_hybridtRNA_2_LSU.mrc as #3.5, grid size 288,288,288, pixel 1.16,
shown at level 2, step 2, values float32
Opened 70S_hybridtRNA_2_atrna.mrc as #3.6, grid size 288,288,288, pixel 1.16,
shown at level 2, step 2, values float32
Opened 70S_hybridtRNA_2_ptrna.mrc as #3.7, grid size 288,288,288, pixel 1.16,
shown at level 2, step 2, values float32
Opened 70S_hybridtRNA_2_apra.mrc as #3.8, grid size 288,288,288, pixel 1.16,
shown at level 2.5, step 2, values float32
Opened 70S_hybridtRNA_2_mRNA.mrc as #3.9, grid size 288,288,288, pixel 1.16,
shown at level 3, step 2, values float32
Log from Mon Nov 30 17:55:28 2020UCSF ChimeraX version: 1.2.dev202011201839
(2020-11-20)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1, grid size
512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32
Opened 70S_tRNA_head.mrc as #3, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_body.mrc as #4, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_LSU.mrc as #5, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_atRNA.mrc as #6, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Opened 70S_tRNA_ptRNA.mrc as #7, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Opened 70S_tRNA_mRNA.mrc as #9, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_apra.mrc as #8, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Log from Mon Nov 30 11:09:35 2020UCSF ChimeraX version: 1.2.dev202011201839
(2020-11-20)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1, grid size
512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32
Opened 70S_tRNA_head.mrc as #3, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_body.mrc as #4, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_LSU.mrc as #5, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_atRNA.mrc as #6, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Opened 70S_tRNA_ptRNA.mrc as #7, grid size 512,512,512, pixel 0.652, shown at
level 2.5, step 1, values float32
Opened 70S_tRNA_apra.mrc as #8, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Opened 70S_tRNA_mRNA.mrc as #9, grid size 512,512,512, pixel 0.652, shown at
level 3, step 1, values float32
Log from Mon Nov 30 10:37:01 2020UCSF ChimeraX version: 1.2.dev202011201839
(2020-11-20)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1-session.cxs"
Opened h1_j620_3d288_6A_sharpened_b50.mrc as #1, grid size 288,288,288, pixel
1.16, shown at level 3, step 1, values float32
Opened 70S_hybridtRNA_1_head.mrc as #3, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_body.mrc as #4, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_LSU.mrc as #5, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_atrna.mrc as #6, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_ptrna.mrc as #7, grid size 288,288,288, pixel 1.16,
shown at level 2, step 1, values float32
Opened 70S_hybridtRNA_1_apra.mrc as #8, grid size 288,288,288, pixel 1.16,
shown at level 3, step 1, values float32
Opened 70S_hybridtRNA_1_mRNA.mrc as #9, grid size 288,288,288, pixel 1.16,
shown at level 3, step 1, values float32
Log from Mon Nov 30 09:54:28 2020UCSF ChimeraX version: 1.2.dev202011201839
(2020-11-20)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/h1_j620_3d288_6A_sharpened_b50.mrc"
Opened h1_j620_3d288_6A_sharpened_b50.mrc as #1, grid size 288,288,288, pixel
1.16, shown at level 4.15, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_tRNA_c1_RSR-1-coot-4.pdb"
Chain information for 70S_tRNA_c1_RSR-1-coot-4.pdb #2
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
y | No description available
z | No description available
> volume #1 step 1
> hide atoms
> show cartoons
> fitmap #2 inMap #1 resolution 6 metric correlation
Opened 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 as #3, grid size 132,144,132, pixel
2, shown at level 0.107, step 1, values float32
Fit map 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 in map
h1_j620_3d288_6A_sharpened_b50.mrc using 320037 points
correlation = 0.9429, correlation about mean = 0.747, overlap = 3.717e+05
steps = 44, shift = 0.0161, angle = 0.0287 degrees
Position of 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 (#3) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#1) coordinates:
Matrix rotation and translation
0.99999996 0.00016786 0.00023238 -0.06154487
-0.00016776 0.99999990 -0.00041167 0.08234666
-0.00023245 0.00041163 0.99999989 -0.03060270
Axis 0.82062428 0.46331615 -0.33453540
Axis point 0.00000000 76.11965950 202.39508680
Rotation angle (degrees) 0.02874101
Shift along axis -0.00211499
> volume #1 level 3
> fitmap #2 inMap #1 resolution 6 metric correlation
Fit map 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 in map
h1_j620_3d288_6A_sharpened_b50.mrc using 320037 points
correlation = 0.9429, correlation about mean = 0.747, overlap = 3.717e+05
steps = 44, shift = 0.0213, angle = 0.00769 degrees
Position of 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 (#3) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#1) coordinates:
Matrix rotation and translation
0.99999994 0.00016524 0.00030974 -0.06304754
-0.00016515 0.99999994 -0.00030211 0.08008564
-0.00030979 0.00030206 0.99999991 -0.00692487
Axis 0.65224867 0.66884412 -0.35667804
Axis point -5.25527793 0.00000000 234.94764095
Rotation angle (degrees) 0.02653600
Shift along axis 0.01491208
> close #3
> hide #!1 models
> select #1/A-Z
Nothing selected
> select #2/A-Z
88932 atoms, 96739 bonds, 422 pseudobonds, 6418 residues, 2 models selected
> select #1/A-Z /0-6
Nothing selected
> select #2/A-Z /0-6
92140 atoms, 99978 bonds, 433 pseudobonds, 6872 residues, 2 models selected
> volume zone #2 nearAtoms sel range 4 newMap true
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #3, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> set bgColor white
> set bgColor black
> close #3
> select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i
15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #3, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/a-u,y-z
52213 atoms, 56371 bonds, 176 pseudobonds, 4043 residues, 2 models selected
> select #2/a-u
51962 atoms, 56095 bonds, 176 pseudobonds, 4030 residues, 2 models selected
> ~select #1/a:929-1068,1107-1381 /s,n,c,j,m,g,i
51962 atoms, 56095 bonds, 176 pseudobonds, 4030 residues, 2 models selected
> hide #!2 models
> show #!2 models
> ~select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i
36124 atoms, 39101 bonds, 170 pseudobonds, 2734 residues, 2 models selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #4, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> hide #!4 models
> show #!4 models
> hide #!2 models
> set bgColor white
> show #!2 models
> hide #!3 models
> hide #!4 models
> select #2/A-Z /0-6
92140 atoms, 99978 bonds, 433 pseudobonds, 6872 residues, 2 models selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #5, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> show #!3 models
> show #!4 models
> hide #!2 models
> volume #3 level 4
> volume #3 level 2
> volume #3 level 3.5
> volume #3 level 3
> volume #3 level 2.5
> show #!2 models
> hide #!2 models
> volume #3 level 2
> show #!2 models
> hide #!2 models
> select #2/x
Nothing selected
> show #!2 models
> select #1/w /y
Nothing selected
> select #2/w /y
1658 atoms, 1843 bonds, 84 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #6, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> select #2/v
1643 atoms, 1834 bonds, 78 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #7, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/A:2001
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #8, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #9, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> color #9 green
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!2 models
> show #!2 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> cartoon style nucleic width 1.5 thickness 1.5 xsection oval
> cartoon style helix width 3 thickness 0.8
> cartoon style strand width 3 thickness 0.8
> cartoon style coil width 0.8 thickness 0.8
> size sel stickRadius 0.25
Changed 0 bond radii
> graphics silhouettes width 1.2
> graphics silhouettes true
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!2 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!2 models
> show #!8 models
> select #1/A:2001
Nothing selected
> show atoms
> hide atoms
> hide #!8 models
> select #1/A:2001
Nothing selected
> select #2/A:2001
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> view name 1
> volume #4 level 2
> show #!2 models
> volume #4 level 2.5
> hide #!2 models
> volume #3 level 2.5
> volume #3 level 2
> volume #3 level 2.3
> volume #3 level 2.5
> volume #3 level 2
> volume #4 level 2
> volume #5 level 2
> volume #5 level 2.5
> volume #5 level 2
> show #!2 models
> view 1
> hide #!2 models
> volume #5 level 2.5
> volume #4 level 2.5
> volume #3 level 2.5
> volume #3 level 2
> volume #3 level 2.3
> volume #3 level 2.5
> volume #3 level 2
> volume #4 level 2
> volume #5 level 2
> volume #6 level 2.5
> volume #6 level 2
> volume #6 level 1.7
> volume #6 level 2
> volume #6 level 1.8
> volume #6 level 2
> view 1
> volume #6 level 1.8
> volume #7 level 1.8
> volume #7 level 2
> volume #6 level 2
> surface dust #6 5
Expected a keyword
> surface dust #6 size 3
> surface dust #6 size 5
> surface dust #6 size 7
> surface dust #6 size 10
> surface dust #6 size 8
> volume #8 level 2
> volume #8 level 3.5
> volume #8 level 3
> view 1
> volume #6 level 2.5
> volume #6 level 2
> view 1
> cd
Current working directory is: C:\Users\anasc
> save 70S_hybridtRNA_1_head.mrc models #3
> save 70S_hybridtRNA_1_body.mrc models #3
> save 70S_hybridtRNA_1_body.mrc models #4
> save 70S_hybridtRNA_1_body.mrc models #4
> save 70S_hybridtRNA_1_head.mrc models #3
> save 70S_hybridtRNA_1_LSU.mrc models #5
> save 70S_hybridtRNA_1_atrna.mrc models #6
> save 70S_hybridtRNA_1_ptrna.mrc models #7
> save 70S_hybridtRNA_1_apra.mrc models #8
> save 70S_hybridtRNA_1_mRNA.mrc models #9
> surface dust #6 size 5
> surface dust #6 size 8
> view 1
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1-view1.png"
> width 4000 height 2343 supersample 4
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1-session.cxs"
> includeMaps true
——— End of log from Mon Nov 30 09:54:28 2020 ———
opened ChimeraX session
> close #2-9
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc"
Opened h2_j621_3d288_95A_sharpened.mrc as #2, grid size 288,288,288, pixel
1.16, shown at level 4.17, step 2, values float32
> close #1
> rename #2 id #1
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2
-Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
1622 messages similar to the above omitted
Ignored bad PDB record found on line 148850
END
Chain information for 70S_tRNA_c2.pdb #2
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
y | No description available
z | No description available
> hide atoms
> show cartoons
> volume #1 step 1
> volume #1 level 3
> volume #1 level 2.224
> fitmap #2 inMap #1 resolution 9.5 metric correlation
Opened 70S_tRNA_c2.pdb map 9.5 as #3, grid size 90,98,90, pixel 3.17, shown at
level 0.0946, step 1, values float32
Fit map 70S_tRNA_c2.pdb map 9.5 in map h2_j621_3d288_95A_sharpened.mrc using
101575 points
correlation = 0.8582, correlation about mean = 0.6472, overlap = 7.552e+04
steps = 56, shift = 0.186, angle = 0.698 degrees
Position of 70S_tRNA_c2.pdb map 9.5 (#3) relative to
h2_j621_3d288_95A_sharpened.mrc (#1) coordinates:
Matrix rotation and translation
0.99994789 0.00899770 0.00482375 -2.39617210
-0.00896547 0.99993762 -0.00666200 2.59597039
-0.00488340 0.00661841 0.99996617 -0.12309569
Axis 0.54523531 0.39853294 -0.73748896
Axis point 295.81443067 257.04759949 0.00000000
Rotation angle (degrees) 0.69779988
Shift along axis -0.18111622
> close #3
> select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i
15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> volume zone #(map) nearAtoms sel range 4 newMap true
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #3, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> cartoon style nucleic width 1.5 thickness 1.5 xsection oval
> cartoon style helix width 3 thickness 0.8
> cartoon style strand width 3 thickness 0.8
> cartoon style coil width 0.8 thickness 0.8
> size sel stickRadius 0.25
Changed 16994 bond radii
> graphics silhouettes width 1.2
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 1.2
> select #2/a-u
51962 atoms, 56095 bonds, 159 pseudobonds, 4030 residues, 2 models selected
> ~select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i
36124 atoms, 39101 bonds, 153 pseudobonds, 2734 residues, 2 models selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #4, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/A-Z /0-6
92140 atoms, 99978 bonds, 402 pseudobonds, 6872 residues, 2 models selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #5, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> hide #!2 models
> show #!2 models
> select #2/w /y
1658 atoms, 1842 bonds, 84 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #6, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/v
1643 atoms, 1834 bonds, 78 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #7, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/A:2001
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #8, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> select #2/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #9, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> hide #!2 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 1.2
> volume #3 level 2
> volume #4 level 2
> volume #5 level 2
> volume #6 level 2
> volume #7 level 2
> volume #8 level 3
> volume #9 level 3
> view 1
> surface dust #6 size 4
> surface dust #6 size 5
> surface dust #6 size 7
> surface dust #6 size 8
> surface dust #5 size 8
> surface dust #5 size 5
> surface dust #5 size 6
> surface dust #5 size 7
> surface dust #5 size 8
> surface dust #3 size 8
> surface dust #4 size 8
> view 1
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2-view1.png"
> width 4000 height 2343 supersample 4
> save 70S_hybridtRNA_2_head.mrc models #3
> save 70S_hybridtRNA_2_body.mrc models #4
> save 70S_hybridtRNA_2_LSU.mrc models #5
> save 70S_hybridtRNA_2_atrna.mrc models #6
> save 70S_hybridtRNA_2_ptrna.mrc models #7
> save 70S_hybridtRNA_2_apra.mrc models #8
> save 70S_hybridtRNA_2_mRNA.mrc models #9
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2-session.cxs"
> includeMaps true
> close #2-9
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_APtRNA_job536_3d512_235A_sharpened_a.mrc"
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #2, grid size
512,512,512, pixel 0.652, shown at level 5.08, step 2, values float32
> close #1
> rename #2 id #1
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_AP_v2.cif-coot-2.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2
-Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_AP_v2.cif-coot-2.pdb
---
warning | Ignored bad PDB record found on line 147610
END
Chain information for 70S_AP_v2.cif-coot-2.pdb #2
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
y | No description available
z | No description available
> hide atoms
> show cartoons
> cartoon style nucleic width 1.5 thickness 1.5 xsection oval
> cartoon style helix width 3 thickness 0.8
> cartoon style strand width 3 thickness 0.8
> cartoon style coil width 0.8 thickness 0.8
> size sel stickRadius 0.25
Changed 0 bond radii
> graphics silhouettes width 1.2
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 1.2
> select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i
15838 atoms, 16994 bonds, 1296 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #3, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> select #2/a-u
51956 atoms, 56095 bonds, 4024 residues, 1 model selected
> ~select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i
36118 atoms, 39101 bonds, 2728 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #4, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> select #2/A-Z /0-6
92129 atoms, 99979 bonds, 6860 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #5, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> select #2/w /y
1652 atoms, 1842 bonds, 78 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #6, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> select #2/v
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #7, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> select #2/A:2001
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #8, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> select #2/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #9, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> hide #2 models
> view 1
> view 1
> view name 2
> volume #3 step 1
> volume #4 step 1
> volume #1 step 1
> volume #5 step 1
> volume #6 step 1
> volume #7 step 1
> volume #8 step 1
> volume #9 step 1
> volume #3 level 2
> volume #3 level 3
> volume #3 level 3.5
> volume #3 level 3.2
> volume #3 level 3.3
> volume #3 level 2
> volume #3 level 2.5
> show #2 models
> hide #2 models
> volume #4 level 2.5
> volume #4 level 2
> volume #4 level 3
> volume #4 level 2.5
> volume #5 level 2.5
> volume #5 level 2
> volume #5 level 3
> volume #4 level 3
> volume #3 level 3
> volume #6 level 2
> volume #6 level 3
> volume #6 level 2.5
> volume #6 level 2
> volume #6 level 2.5
> volume #7 level 2.5
> volume #7 level 3
> volume #7 level 2.5
> volume #8 level 3
> volume #9 level 3
> view 2
> view name 2
> view 2
> surface dust #6 size 8
> surface dust #6 size 5
> surface dust #5 size 5
> surface dust #7 size 5
> surface dust #8 size 5
> surface dust #3 size 5
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-view2.png" width
> 4000 height 2343 supersample 4
> save 70S_tRNA_head.mrc models #3
> save 70S_tRNA_body.mrc models #4
> save 70S_tRNA_LSU.mrc models #5
> save 70S_tRNA_atRNA.mrc models #6
> save 70S_tRNA_ptRNA.mrc models #7
> save 70S_tRNA_apra.mrc models #8
> save 70S_tRNA_mRNA.mrc models #9
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"
> includeMaps true
——— End of log from Mon Nov 30 10:37:01 2020 ———
opened ChimeraX session
> select #2/a:2001
37 atoms, 40 bonds, 1 residue, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #10, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> hide #!8 models
> volume #10 level 2.5
> close #8
> rename #10 id #8
> cd
Current working directory is: C:\Users\anasc
> save 70S_tRNA_apra.mrc models #8
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-view2.png" width
> 4000 height 2343 supersample 4
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"
> includeMaps true
——— End of log from Mon Nov 30 11:09:35 2020 ———
opened ChimeraX session
> rename #1-9 id #11
> rename #11 70S_APtRNA
> rename #11 id #1
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/h1_j620_3d288_6A_sharpened_b50.mrc"
Opened h1_j620_3d288_6A_sharpened_b50.mrc as #2, grid size 288,288,288, pixel
1.16, shown at level 4.15, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_tRNA_c1_RSR-1-coot-4.pdb"
Chain information for 70S_tRNA_c1_RSR-1-coot-4.pdb #3
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
y | No description available
z | No description available
> hide #!3 atoms
> show #!3 cartoons
> hide #!2 models
> hide #!3 models
> hide #!1 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.7 models
> hide #!1.8 models
> hide #!1.9 models
> show #1.2 models
> show #!3 models
> mmaker #3/A to #1.2/A matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with
70S_tRNA_c1_RSR-1-coot-4.pdb, chain A (#3), sequence alignment score = 11577
RMSD between 2606 pruned atom pairs is 0.808 angstroms; (across all 2903
pairs: 3.806)
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #1.2 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_head.mrc"
Opened 70S_hybridtRNA_1_head.mrc as #4, grid size 288,288,288, pixel 1.16,
shown at level 0.0507, step 2, values float32
> hide #!4 models
> show #!4 models
> select #3/a:929-1068,1107-1381 /s,n,c,j,m,g,i
15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> volume zone #2 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #5, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 step 1
> volume #2 level 3
> volume #2 level 4
> volume #2 level 2
> select #3/a:929-1068,1107-1381 /s,n,c,j,m,g,i
15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected
> volume zone #2 nearAtoms sel range 4 newMap true
Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #6, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> hide #!5 models
> close #5
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 step 1
> volume #4 level 2
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> close #6
> hide #!3 models
> show #!3 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_body.mrc"
Opened 70S_hybridtRNA_1_body.mrc as #5, grid size 288,288,288, pixel 1.16,
shown at level 2.07, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_LSU.mrc"
Opened 70S_hybridtRNA_1_LSU.mrc as #6, grid size 288,288,288, pixel 1.16,
shown at level 3.71, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_atrna.mrc"
Opened 70S_hybridtRNA_1_atrna.mrc as #7, grid size 288,288,288, pixel 1.16,
shown at level 0.000495, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_ptrna.mrc"
Opened 70S_hybridtRNA_1_ptrna.mrc as #8, grid size 288,288,288, pixel 1.16,
shown at level 0.000511, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_apra.mrc"
Opened 70S_hybridtRNA_1_apra.mrc as #9, grid size 288,288,288, pixel 1.16,
shown at level 6.88e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_mRNA.mrc"
Opened 70S_hybridtRNA_1_mRNA.mrc as #10, grid size 288,288,288, pixel 1.16,
shown at level 0.000595, step 2, values float32
> select #5-10
12 models selected
> volume sel step 1
> show #!4 models
> volume #5 level 2
> volume #6 level 2
> volume #7 level 2
> hide #!3 models
> volume #8 level 2
> volume #9 level 2.5
> volume #10 level 3
> ui mousemode right select
> select clear
> surface dust #6 size 5
> surface dust #7 size 5
> surface dust #7 size 7
> surface dust #8 size 7
> view 2
> rename #2-10 id #11
> rename #11 70S_hybridtRNA_1
> rename #11 #2
No name or id option specified for renaming
> rename #11 id #2
> show #!2.2 models
> hide #!2.2 models
> show #1.2 models
> hide #1.2 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc"
Opened h2_j621_3d288_95A_sharpened.mrc as #3, grid size 288,288,288, pixel
1.16, shown at level 4.17, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2
-Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
1622 messages similar to the above omitted
Ignored bad PDB record found on line 148850
END
Chain information for 70S_tRNA_c2.pdb #4
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
y | No description available
z | No description available
> hide #!4 atoms
> show #!4 cartoons
> hide #!3 models
> hide #!2.9 models
> show #!3 models
> hide #!2.8 models
> hide #!2.7 models
> hide #!2.6 models
> hide #!2.5 models
> hide #!2.4 models
> hide #!2.3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #1.2 models
> mmaker #4/A to #1.2/A matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with 70S_tRNA_c2.pdb,
chain A (#4), sequence alignment score = 11577
RMSD between 2718 pruned atom pairs is 0.450 angstroms; (across all 2903
pairs: 3.635)
> show #!2.2 models
> hide #!2.2 models
> show #!3 models
> close #3
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc"
Opened h2_j621_3d288_95A_sharpened.mrc as #3, grid size 288,288,288, pixel
1.16, shown at level 4.17, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_head.mrc"
Opened 70S_hybridtRNA_2_head.mrc as #5, grid size 288,288,288, pixel 1.16,
shown at level 0.00115, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_body.mrc"
Opened 70S_hybridtRNA_2_body.mrc as #6, grid size 288,288,288, pixel 1.16,
shown at level 2.1, step 2, values float32
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #1.2 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_LSU.mrc"
Opened 70S_hybridtRNA_2_LSU.mrc as #7, grid size 288,288,288, pixel 1.16,
shown at level 3.69, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_atrna.mrc"
Opened 70S_hybridtRNA_2_atrna.mrc as #8, grid size 288,288,288, pixel 1.16,
shown at level 0.00072, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_ptrna.mrc"
Opened 70S_hybridtRNA_2_ptrna.mrc as #9, grid size 288,288,288, pixel 1.16,
shown at level 7.04e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_apra.mrc"
Opened 70S_hybridtRNA_2_apra.mrc as #10, grid size 288,288,288, pixel 1.16,
shown at level 8.03e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_mRNA.mrc"
Opened 70S_hybridtRNA_2_mRNA.mrc as #11, grid size 288,288,288, pixel 1.16,
shown at level 0.000295, step 2, values float32
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> ui mousemode right translate
> volume #3 step 1
> select #5-11
14 models selected
> hide #!4 models
> volume sel step 1
> show #!4 models
> hide #!4 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> show #!4 models
> select #4/a-u
51962 atoms, 56095 bonds, 159 pseudobonds, 4030 residues, 2 models selected
> ~select #4/a:929-1068,1107-1381 /s,n,c,j,m,g,i
36124 atoms, 39101 bonds, 153 pseudobonds, 2734 residues, 2 models selected
> volume zone #3 nearAtoms sel range 4 newMap true
Opened h2_j621_3d288_95A_sharpened.mrc zone as #12, grid size 288,288,288,
pixel 1.16, shown at step 1, values float32
> show #!3 models
> hide #!12 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!4 models
> volume #3 level 3
> show #!1.1 models
> hide #!1.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> show #!5 models
> hide #!4 models
> show #!4 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> close #12
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #5.1 models
> show #!5 models
> hide #!5 models
> close #5
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_head.mrc"
Opened 70S_hybridtRNA_2_head.mrc as #5, grid size 288,288,288, pixel 1.16,
shown at level 0.00115, step 2, values float32
> select #5
2 models selected
> close #5
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> close #6-11
> hide #!2.3 models
> hide #!2.4 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_head.mrc"
Opened 70S_hybridtRNA_2_head.mrc as #5, grid size 288,288,288, pixel 1.16,
shown at level 0.00115, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_body.mrc"
Opened 70S_hybridtRNA_2_body.mrc as #6, grid size 288,288,288, pixel 1.16,
shown at level 2.1, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_LSU.mrc"
Opened 70S_hybridtRNA_2_LSU.mrc as #7, grid size 288,288,288, pixel 1.16,
shown at level 3.69, step 2, values float32
> show #!4 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_atrna.mrc"
Opened 70S_hybridtRNA_2_atrna.mrc as #8, grid size 288,288,288, pixel 1.16,
shown at level 0.00072, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_ptrna.mrc"
Opened 70S_hybridtRNA_2_ptrna.mrc as #9, grid size 288,288,288, pixel 1.16,
shown at level 7.04e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_apra.mrc"
Opened 70S_hybridtRNA_2_apra.mrc as #10, grid size 288,288,288, pixel 1.16,
shown at level 8.03e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_mRNA.mrc"
Opened 70S_hybridtRNA_2_mRNA.mrc as #11, grid size 288,288,288, pixel 1.16,
shown at level 0.000295, step 2, values float32
> hide #!4 models
> hide #!6 models
> show #!6 models
> volume #1.4 level 2
> volume #1.5 level 2
> hide #!7 models
> show #!7 models
> select #5
2 models selected
> volume sel level 2
> select #6
2 models selected
> volume sel level 2
> select #7
2 models selected
> volume sel level 2
> select #8
2 models selected
> volume sel level 2
> select #9
2 models selected
> volume sel level 2
> select #10
2 models selected
> volume sel level 2.5
> select #11
2 models selected
> volume sel level 3
> surface dust #6 size 5
> surface dust #7 size 5
> surface dust #8 size 5
> surface dust #9 size 5
> rename #3-11 id #12
> rename #12 70S_hybridtRNA_2
> rename #12 id #3
> hide #!1 models
> hide #!2 models
> hide #!3 models
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/all_states-session.cxs" includeMaps
> true
——— End of log from Mon Nov 30 17:55:28 2020 ———
opened ChimeraX session
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-
> Pi_job1086_3d512_31A_sharpened.mrc"
Opened pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc as #4, grid size
512,512,512, pixel 0.652, shown at level 4.33, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/Pre1_GDP-
> Pi_RSR-4-coot-42.pdb"
Chain information for Pre1_GDP-Pi_RSR-4-coot-42.pdb #5
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide #!4 models
> hide #5 atoms
> show #5 cartoons
> mmaker #5/A to #1.2/A matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with Pre1_GDP-
Pi_RSR-4-coot-42.pdb, chain A (#5), sequence alignment score = 11579.8
RMSD between 2721 pruned atom pairs is 0.483 angstroms; (across all 2903
pairs: 3.598)
> show #1.2 models
> hide #1.2 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_head.mrc"
Opened pre1_GDP-Pi_head.mrc as #6, grid size 512,512,512, pixel 0.652, shown
at level 0.00136, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_body.mrc"
Opened pre1_GDP-Pi_body.mrc as #7, grid size 512,512,512, pixel 0.652, shown
at level 1.55, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_LSU.mrc"
Opened pre1_GDP-Pi_LSU.mrc as #8, grid size 512,512,512, pixel 0.652, shown at
level 3.48, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_atrna.mrc"
Opened pre1_GDP-Pi_atrna.mrc as #9, grid size 512,512,512, pixel 0.652, shown
at level 0.00121, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_ptrna.mrc"
Opened pre1_GDP-Pi_ptrna.mrc as #10, grid size 512,512,512, pixel 0.652, shown
at level 0.00111, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_EFG.mrc"
Opened pre1_GDP-Pi_EFG.mrc as #11, grid size 512,512,512, pixel 0.652, shown
at level 0.0012, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_apra.mrc"
Opened pre1_GDP-Pi_apra.mrc as #12, grid size 512,512,512, pixel 0.652, shown
at level 0.000806, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_mrna.mrc"
Opened pre1_GDP-Pi_mrna.mrc as #13, grid size 512,512,512, pixel 0.652, shown
at level 0.000387, step 2, values float32
> volume #3.3 step 1
> hide #5 models
> volume #3.4 step 1
> volume #3.5 step 1
> volume #3.6 step 1
> volume #3.7 step 1
> volume #3.8 step 1
> volume #3.9 step 1
> volume #4 step 1
> volume #6 step 1
> volume #7 step 1
> 2dlabels
> volume #7 level 2.5
> hide #!6 models
> show #!6 models
> hide #!1 models
> volume #6 level 2.5
> volume #8 step 1
> volume #8 level 2.5
> volume #9 step 1
> volume #9 level 2.5
> volume #10 step 1
> volume #10 level 2.5
> volume #11 step 1
> volume #11 level 2.52
> volume #11 level 2.5
> volume #12 step 1
> volume #12 level 2.5
> volume #13 step 1
> volume #13 level 3
> view 2
> rename #6-13 id #14
> rename #4 id #14.9
> rename #5 id #14.10
> rename #14 Pre1_GDP-Pi
> rename #14 #4
No name or id option specified for renaming
> rename #14 id #4
> hide #!4.8 models
> hide #!4.7 models
> hide #!4.6 models
> hide #!4.5 models
> hide #!4.4 models
> hide #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/all_states-session-2.cxs"
> includeMaps true
——— End of log from Mon Nov 30 18:33:50 2020 ———
opened ChimeraX session
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> show #!4.2 models
> show #!4.3 models
> show #!4.4 models
> show #!4.5 models
> show #!4.6 models
> show #!4.7 models
> show #!4.8 models
> show #!4.9 models
> hide #!4.9 models
> hide #!4.8 models
> hide #!4.7 models
> hide #!4.6 models
> hide #!4.5 models
> hide #!4.4 models
> hide #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-
> Pi_job918_5A_sharpened_b100.mrc"
Opened pre2_GDP-Pi_job918_5A_sharpened_b100.mrc as #5, grid size 288,288,288,
pixel 1.16, shown at level 3.62, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/Pre2_GDP-
> Pi_RSR-0-coot-6.pdb"
Chain information for Pre2_GDP-Pi_RSR-0-coot-6.pdb #6
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide #!6 atoms
> show #!6 cartoons
> volume #5 step 1
> volume #5 level 2.442
> hide #!6 models
> show #!6 models
> hide #!5 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_head.mrc"
Opened pre2_GDP-Pi_head.mrc as #7, grid size 288,288,288, pixel 1.16, shown at
level 0.146, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_body.mrc"
Opened pre2_GDP-Pi_body.mrc as #8, grid size 288,288,288, pixel 1.16, shown at
level 1.81, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_LSU.mrc"
Opened pre2_GDP-Pi_LSU.mrc as #9, grid size 288,288,288, pixel 1.16, shown at
level 3.21, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_atrna.mrc"
Opened pre2_GDP-Pi_atrna.mrc as #10, grid size 288,288,288, pixel 1.16, shown
at level 0.000352, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_ptrna.mrc"
Opened pre2_GDP-Pi_ptrna.mrc as #11, grid size 288,288,288, pixel 1.16, shown
at level 5.82e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_EFG.mrc"
Opened pre2_GDP-Pi_EFG.mrc as #12, grid size 288,288,288, pixel 1.16, shown at
level 0.000251, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_apra.mrc"
Opened pre2_GDP-Pi_apra.mrc as #13, grid size 288,288,288, pixel 1.16, shown
at level 0.00035, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_mrna.mrc"
Opened pre2_GDP-Pi_mrna.mrc as #14, grid size 288,288,288, pixel 1.16, shown
at level 0.000594, step 2, values float32
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!6 models
> show #!6 models
> mmaker #6/A to #1.2/A matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with Pre2_GDP-
Pi_RSR-0-coot-6.pdb, chain A (#6), sequence alignment score = 11579.8
RMSD between 2684 pruned atom pairs is 0.593 angstroms; (across all 2903
pairs: 3.693)
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!5 models
> close #5
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-
> Pi_job918_5A_sharpened_b100.mrc"
Opened pre2_GDP-Pi_job918_5A_sharpened_b100.mrc as #5, grid size 288,288,288,
pixel 1.16, shown at level 3.62, step 2, values float32
> volume #5 step 1
> volume #5 level 2
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!7 models
Must specify one map, got 0
> show #!5 models
> hide #!5 models
> show #1.2 models
> hide #1.2 models
> show #!5 models
> show #!8 models
> hide #!5 models
> hide #!6 models
> volume #7 level 2
> volume #8 level 2
> show #!9 models
> volume #9 level 2
> show #!10 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!14 models
> volume #10 level 2
> volume #11 level 2
> volume #12 level 2
> volume #13 level 2
> volume #14 level 2
> volume #14 level 3
> volume #13 level 2.5
> volume #12 level 2.5
> volume #12 level 2
> view 2
> surface dust #7 size 5
> surface dust #8 size 5
> surface dust #9 size 5
> surface dust #10 size 5
> surface dust #11 size 5
> surface dust #12 size 5
> surface dust #12 size 3
> view 2
> rename #5-14 id #15
> rename #15 Pre2_GDP-Pi
> rename #15 id #5
> hide #!1 models
> hide #!5 models
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/all_states-session-3.cxs"
> includeMaps true
> volume #5.10 step 1
> volume #5.9 step 1
> volume #5.8 step 1
> volume #5.7 step 1
> volume #5.6 step 1
> volume #5.5 step 1
> volume #5.4 step 1
> volume #5.3 step 1
> show #!5 models
> hide #!5 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc"
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #6, grid size
512,512,512, pixel 0.652, shown at level 4.2, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/Chimeric_GDP-1-sw1-v2-RSR-0-coot-10.pdb"
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-10.pdb #7
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide #7 atoms
> show #7 cartoons
> volume #6 step 1
> hide #!6 models
> mmaker #7/A to #1.2/A matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with
Chimeric_GDP-1-sw1-v2-RSR-0-coot-10.pdb, chain A (#7), sequence alignment
score = 11574.9
RMSD between 2736 pruned atom pairs is 0.476 angstroms; (across all 2903
pairs: 3.121)
> show #!6 models
> close #6
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc"
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #6, grid size
512,512,512, pixel 0.652, shown at level 4.2, step 2, values float32
> volume #6 step 1
> volume #6 level 3
> hide #!6 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_head.mrc"
Opened chimeric_GDP1_head.mrc as #8, grid size 512,512,512, pixel 0.652, shown
at level 0.000896, step 2, values float32
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> hide #!1 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_body.mrc"
Opened chimeric_GDP1_body.mrc as #9, grid size 512,512,512, pixel 0.652, shown
at level 1.58, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_LSU.mrc"
Opened chimeric_GDP1_LSU.mrc as #10, grid size 512,512,512, pixel 0.652, shown
at level 3.46, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_atrna.mrc"
Opened chimeric_GDP1_atrna.mrc as #11, grid size 512,512,512, pixel 0.652,
shown at level 0.00118, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_ptrna.mrc"
Opened chimeric_GDP1_ptrna.mrc as #12, grid size 512,512,512, pixel 0.652,
shown at level 0.000534, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_EFG.mrc"
Opened chimeric_GDP1_EFG.mrc as #13, grid size 512,512,512, pixel 0.652, shown
at level 0.000524, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_apra.mrc"
Opened chimeric_GDP1_apra.mrc as #14, grid size 512,512,512, pixel 0.652,
shown at level 0.000586, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_mrna.mrc"
Opened chimeric_GDP1_mrna.mrc as #15, grid size 512,512,512, pixel 0.652,
shown at level 0.000791, step 2, values float32
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!6 models
> hide #!6 models
> hide #7#!8-15 target m
> show #!1 models
> hide #!1 models
> show #!1.1 models
> show #1.2 models
> volume #1.1 level 3
> hide #!1 models
> show #!2.1 models
> show #!2.2 models
> hide #!2 models
> show #!4.9 models
> show #4.10 models
> volume #4.9 level 3
> show #!4.6 models
> hide #!4.6 models
> show #!4.6 models
> hide #!4.6 models
> hide #1.2 models
> hide #!4 models
> hide #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!1.1 models
> show #!1.1 models
> fitmap #2.1 inMap #1.1
Fit map h1_j620_3d288_6A_sharpened_b50.mrc in map
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 1019265 points
correlation = 0.758, correlation about mean = 0.3486, overlap = 1.039e+07
steps = 148, shift = 0.333, angle = 2.26 degrees
Position of h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) relative to
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99938269 -0.01003340 -0.03366867 7.22159598
0.01062870 0.99978951 0.01754891 -4.68556235
0.03348551 -0.01789593 0.99927897 -2.24962642
Axis -0.45040638 -0.85334473 0.26255830
Axis point 73.03250787 0.00000000 215.22572937
Rotation angle (degrees) 2.25503531
Shift along axis 0.15508892
> show #!1.3 models
> hide #!1.3 models
> show #!2.3 models
> hide #!2.3 models
> hide #!1.1 models
> show #!2.3 models
> show #!2.4 models
> show #!2.5 models
> hide #!2.5 models
> hide #!2.4 models
> hide #!2.3 models
> fitmap #2.3 inMap #2.1
Fit map 70S_hybridtRNA_1_head.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 106926 points
correlation = 0.9999, correlation about mean = 0.9992, overlap = 1.181e+06
steps = 68, shift = 2.22, angle = 2.32 degrees
Position of 70S_hybridtRNA_1_head.mrc (#2.3) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99999913 0.00018464 -0.00130857 0.30474276
-0.00018435 0.99999996 0.00022176 -0.01583817
0.00130861 -0.00022152 0.99999912 -0.19904439
Axis -0.16540569 -0.97656743 -0.13768446
Axis point 153.05191918 0.00000000 231.82731819
Rotation angle (degrees) 0.07677596
Shift along axis -0.00753383
> fitmap #2.4 inMap #2.1
Fit map 70S_hybridtRNA_1_body.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 248174 points
correlation = 1, correlation about mean = 0.9999, overlap = 3.058e+06
steps = 60, shift = 1.36, angle = 2.26 degrees
Position of 70S_hybridtRNA_1_body.mrc (#2.4) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99999999 0.00000073 -0.00015435 0.02008714
-0.00000074 1.00000000 -0.00004725 0.00026928
0.00015435 0.00004725 0.99999999 -0.00563801
Axis 0.29271365 -0.95618922 -0.00457120
Axis point 36.37090414 0.00000000 119.42835544
Rotation angle (degrees) 0.00924864
Shift along axis 0.00564807
> fitmap #2.5 inMap #2.1
Fit map 70S_hybridtRNA_1_LSU.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 645850 points
correlation = 1, correlation about mean = 1, overlap = 8.787e+06
steps = 76, shift = 0.496, angle = 2.26 degrees
Position of 70S_hybridtRNA_1_LSU.mrc (#2.5) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
1.00000000 0.00005443 -0.00000811 -0.01818076
-0.00005443 1.00000000 0.00005243 -0.00879512
0.00000811 -0.00005243 1.00000000 0.01425598
Axis -0.68980002 -0.10667675 -0.71609776
Axis point -155.19121641 292.56515973 0.00000000
Rotation angle (degrees) 0.00435502
Shift along axis 0.00327064
> fitmap #2.6 inMap #2.1
Fit map 70S_hybridtRNA_1_atrna.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 10321 points
correlation = 0.9991, correlation about mean = 0.9847, overlap = 9.656e+04
steps = 56, shift = 1.56, angle = 2.48 degrees
Position of 70S_hybridtRNA_1_atrna.mrc (#2.6) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99996704 0.00359830 -0.00727780 0.85823304
-0.00363736 0.99997901 -0.00536105 1.74125940
0.00725836 0.00538734 0.99995915 -2.07663962
Axis 0.55197485 -0.74649232 -0.37158174
Axis point 289.57156341 0.00000000 120.74485176
Rotation angle (degrees) 0.55785807
Shift along axis -0.05447235
> fitmap #2.7 inMap #2.1
Fit map 70S_hybridtRNA_1_ptrna.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 10586 points
correlation = 0.9999, correlation about mean = 0.9979, overlap = 1.079e+05
steps = 56, shift = 2.08, angle = 2.37 degrees
Position of 70S_hybridtRNA_1_ptrna.mrc (#2.7) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99999717 -0.00071957 -0.00226942 0.50780974
0.00071931 0.99999973 -0.00011793 -0.09132956
0.00226950 0.00011630 0.99999742 -0.37367633
Axis 0.04913293 -0.95209666 0.30182428
Axis point 164.78877149 0.00000000 223.57562255
Rotation angle (degrees) 0.13657275
Shift along axis -0.00087984
> fitmap #2.8 inMap #2.1
Fit map 70S_hybridtRNA_1_apra.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 320 points
correlation = 0.9959, correlation about mean = 0.9289, overlap = 4629
steps = 52, shift = 0.689, angle = 3 degrees
Position of 70S_hybridtRNA_1_apra.mrc (#2.8) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99988320 0.01104181 -0.01056739 0.46136207
-0.01093254 0.99988675 0.01034247 0.18375324
0.01068040 -0.01022573 0.99989068 -0.36745969
Axis -0.55826931 -0.57671487 -0.59643553
Axis point 9.54818132 -34.38282742 0.00000000
Rotation angle (degrees) 1.05552809
Shift along axis -0.14437150
> fitmap #2.9 inMap #2.1
Fit map 70S_hybridtRNA_1_mRNA.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc
using 1152 points
correlation = 0.9989, correlation about mean = 0.9566, overlap = 1.747e+04
steps = 72, shift = 0.57, angle = 2.85 degrees
Position of 70S_hybridtRNA_1_mRNA.mrc (#2.9) relative to
h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99979104 -0.01343703 0.01540542 -1.00891360
0.01309125 0.99966492 0.02233096 -6.14975350
-0.01570032 -0.02212461 0.99963193 5.22998756
Axis -0.73607439 0.51503427 0.43924275
Axis point 0.00000000 234.32729021 275.96776812
Rotation angle (degrees) 1.73046623
Shift along axis -0.12746420
> show #!2.7 models
> hide #!2.7 models
> show #!2.5 models
> hide #!2.5 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3.1 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> hide #!3.8 models
> hide #!3.9 models
> show #!1.1 models
> fitmap #3.1 inMap #1.1
Fit map h2_j621_3d288_95A_sharpened.mrc in map
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 586949 points
correlation = 0.7334, correlation about mean = 0.1805, overlap = 7.27e+06
steps = 136, shift = 0.202, angle = 2.83 degrees
Position of h2_j621_3d288_95A_sharpened.mrc (#3.1) relative to
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99916948 -0.01437521 -0.03812740 8.91883158
0.01542745 0.99950415 0.02744894 -7.15808810
0.03771391 -0.02801435 0.99889582 -1.25644332
Axis -0.56267235 -0.76940650 0.30234660
Axis point 41.06042297 0.00000000 234.63921817
Rotation angle (degrees) 2.82500121
Shift along axis 0.10921816
> show #!3.2 models
> hide #!3.1 models
> hide #!3 models
> hide #!1.1 models
> show #1.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> hide #1.2 models
> show #!3.1 models
> hide #!3 models
> show #!3 models
> fitmap #3.3 inMap #3.1
Fit map 70S_hybridtRNA_2_head.mrc in map h2_j621_3d288_95A_sharpened.mrc using
110214 points
correlation = 1, correlation about mean = 0.9997, overlap = 1.309e+06
steps = 72, shift = 2.45, angle = 2.87 degrees
Position of 70S_hybridtRNA_2_head.mrc (#3.3) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
0.99999961 0.00020314 -0.00085583 0.19817180
-0.00020293 0.99999995 0.00024396 -0.02384413
0.00085588 -0.00024379 0.99999960 -0.12304039
Axis -0.26717286 -0.93762481 -0.22243737
Axis point 144.70241929 0.00000000 230.48398110
Rotation angle (degrees) 0.05229911
Shift along axis -0.00322050
> fitmap #3.4 inMap #3.1
Fit map 70S_hybridtRNA_2_body.mrc in map h2_j621_3d288_95A_sharpened.mrc using
251585 points
correlation = 1, correlation about mean = 0.9999, overlap = 3.15e+06
steps = 64, shift = 2.07, angle = 2.81 degrees
Position of 70S_hybridtRNA_2_body.mrc (#3.4) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
0.99999999 -0.00001982 0.00011005 -0.00098565
0.00001984 0.99999998 -0.00017740 0.03316350
-0.00011005 0.00017740 0.99999998 0.01688522
Axis 0.84596406 0.52478712 0.09456899
Axis point 0.00000000 -85.48083137 133.20998322
Rotation angle (degrees) 0.01201495
Shift along axis 0.01816677
> fitmap #3.5 inMap #3.1
Fit map 70S_hybridtRNA_2_LSU.mrc in map h2_j621_3d288_95A_sharpened.mrc using
650695 points
correlation = 1, correlation about mean = 1, overlap = 8.779e+06
steps = 84, shift = 0.298, angle = 2.83 degrees
Position of 70S_hybridtRNA_2_LSU.mrc (#3.5) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
1.00000000 0.00003479 0.00002320 -0.01444674
-0.00003479 1.00000000 0.00005333 -0.01032144
-0.00002319 -0.00005333 1.00000000 0.01078704
Axis -0.78699220 0.34226528 -0.51332033
Axis point 0.00000000 224.38621378 208.29890200
Rotation angle (degrees) 0.00388278
Shift along axis 0.00229959
> fitmap #3.6 inMap #3.1
Fit map 70S_hybridtRNA_2_atrna.mrc in map h2_j621_3d288_95A_sharpened.mrc
using 10628 points
correlation = 0.9997, correlation about mean = 0.9961, overlap = 1.157e+05
steps = 56, shift = 1.74, angle = 2.95 degrees
Position of 70S_hybridtRNA_2_atrna.mrc (#3.6) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
0.99998258 0.00297566 -0.00509681 0.52466684
-0.00298680 0.99999316 -0.00218073 0.98182149
0.00509028 0.00219592 0.99998463 -1.23126425
Axis 0.34765674 -0.80920582 -0.47362511
Axis point 244.89166359 0.00000000 104.07713390
Rotation angle (degrees) 0.36065047
Shift along axis -0.02893404
> fitmap #3.7 inMap #3.1
Fit map 70S_hybridtRNA_2_ptrna.mrc in map h2_j621_3d288_95A_sharpened.mrc
using 11809 points
correlation = 0.9997, correlation about mean = 0.9961, overlap = 1.338e+05
steps = 56, shift = 2.34, angle = 2.75 degrees
Position of 70S_hybridtRNA_2_ptrna.mrc (#3.7) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
0.99999179 -0.00346764 0.00209878 -0.02675129
0.00347092 0.99999276 -0.00156038 -0.15370001
-0.00209336 0.00156766 0.99999658 0.03950185
Axis 0.35999174 0.48245407 0.79852615
Axis point 37.01596015 -2.37894752 0.00000000
Rotation angle (degrees) 0.24892805
Shift along axis -0.05224018
> fitmap #3.8 inMap #3.1
Fit map 70S_hybridtRNA_2_apra.mrc in map h2_j621_3d288_95A_sharpened.mrc using
325 points
correlation = 0.9705, correlation about mean = 0.5188, overlap = 3853
steps = 56, shift = 2.17, angle = 15.3 degrees
Position of 70S_hybridtRNA_2_apra.mrc (#3.8) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
0.95381646 0.17724187 0.24252727 -59.19928960
-0.16152211 0.98333887 -0.08339834 43.03541118
-0.25326816 0.04037319 0.96655328 40.46604137
Axis 0.20187770 0.80866769 -0.55254136
Axis point 125.40431157 0.00000000 268.38244402
Rotation angle (degrees) 17.85148710
Shift along axis 0.49116838
> fitmap #3.9 inMap #3.1
Fit map 70S_hybridtRNA_2_mRNA.mrc in map h2_j621_3d288_95A_sharpened.mrc using
1190 points
correlation = 0.9991, correlation about mean = 0.9754, overlap = 1.781e+04
steps = 72, shift = 0.734, angle = 3 degrees
Position of 70S_hybridtRNA_2_mRNA.mrc (#3.9) relative to
h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates:
Matrix rotation and translation
0.99994023 -0.00597422 0.00915666 -0.72792573
0.00587457 0.99992364 0.01087173 -2.82053734
-0.00922091 -0.01081729 0.99989898 2.95444519
Axis -0.70422514 0.59670496 0.38472086
Axis point 0.00000000 271.90008851 259.49403869
Rotation angle (degrees) 0.88234435
Shift along axis -0.03376831
> show #!3.4 models
> hide #!3.4 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.6 models
> hide #!3.6 models
> show #!1.1 models
> hide #!1.1 models
> show #1.2 models
> hide #!3.1 models
> show #!3.2 models
> hide #!3.2 models
> hide #!3 models
> hide #4.10 models
> show #4.10 models
> hide #4.10 models
> hide #!4.9 models
> show #!4.9 models
> hide #!4.9 models
> show #4.10 models
> hide #4.10 models
> show #!4.9 models
> fitmap #4.9 inMap #1.1
Fit map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc in map
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 2630225 points
correlation = 0.8573, correlation about mean = 0.5417, overlap = 5.626e+07
steps = 156, shift = 0.796, angle = 2.99 degrees
Position of pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc (#4.9) relative to
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99919851 -0.00239100 -0.03995767 7.07517244
0.00372795 0.99943450 0.03341822 -6.28809111
0.03985517 -0.03354040 0.99864238 -0.16494756
Axis -0.64161263 -0.76478454 0.05863309
Axis point 10.68733214 0.00000000 181.02472824
Rotation angle (degrees) 2.99104905
Shift along axis 0.25984353
> show #!1.1 models
> hide #!1.1 models
> hide #1.2 models
> fitmap #4.1 inMap #4.9
Fit map pre1_GDP-Pi_head.mrc in map pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc using 347242 points
correlation = 1, correlation about mean = 0.9997, overlap = 5.734e+06
steps = 68, shift = 3.81, angle = 3.02 degrees
Position of pre1_GDP-Pi_head.mrc (#4.1) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
0.99999988 0.00009386 -0.00049056 0.11232562
-0.00009376 0.99999997 0.00020958 -0.03518945
0.00049058 -0.00020953 0.99999986 -0.05502258
Axis -0.38688943 -0.90571423 -0.17320021
Axis point 112.94959002 0.00000000 227.32288231
Rotation angle (degrees) 0.03103376
Shift along axis -0.00205609
> fitmap #4.2 inMap #4.9
Fit map pre1_GDP-Pi_body.mrc in map pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc using 813215 points
correlation = 1, correlation about mean = 1, overlap = 1.676e+07
steps = 96, shift = 1.89, angle = 2.99 degrees
Position of pre1_GDP-Pi_body.mrc (#4.2) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
1.00000000 0.00001201 0.00005463 -0.00655600
-0.00001201 1.00000000 0.00005452 -0.00597151
-0.00005463 -0.00005452 1.00000000 0.01524047
Axis -0.69798069 0.69942157 -0.15372840
Axis point 273.49811090 0.00000000 144.84438871
Rotation angle (degrees) 0.00447527
Shift along axis -0.00194353
> fitmap #4.3 inMap #4.9
Fit map pre1_GDP-Pi_LSU.mrc in map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc
using 2109177 points
correlation = 1, correlation about mean = 1, overlap = 5.063e+07
steps = 84, shift = 0.466, angle = 2.99 degrees
Position of pre1_GDP-Pi_LSU.mrc (#4.3) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
1.00000000 0.00002399 0.00001315 -0.00611672
-0.00002399 1.00000000 0.00000004 0.00601174
-0.00001315 -0.00000004 1.00000000 -0.00165998
Axis -0.00140942 0.48065645 -0.87690786
Axis point 163.35017024 254.70397239 0.00000000
Rotation angle (degrees) 0.00156755
Shift along axis 0.00435385
> fitmap #4.4 inMap #4.9
Fit map pre1_GDP-Pi_atrna.mrc in map pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc using 31295 points
correlation = 0.9987, correlation about mean = 0.9861, overlap = 4.67e+05
steps = 72, shift = 2.49, angle = 2.92 degrees
Position of pre1_GDP-Pi_atrna.mrc (#4.4) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
0.99999613 0.00242962 -0.00135281 -0.06193794
-0.00243446 0.99999062 -0.00358249 1.14611174
0.00134409 0.00358577 0.99999267 -0.75288229
Axis 0.79007845 -0.29725038 -0.53611403
Axis point 0.00000000 208.52431006 320.53712370
Rotation angle (degrees) 0.25991875
Shift along axis 0.01401278
> fitmap #4.5 inMap #4.9
Fit map pre1_GDP-Pi_ptrna.mrc in map pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc using 37262 points
correlation = 0.9998, correlation about mean = 0.9983, overlap = 6.319e+05
steps = 80, shift = 2.58, angle = 3.03 degrees
Position of pre1_GDP-Pi_ptrna.mrc (#4.5) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
0.99999976 -0.00047111 -0.00050364 0.13930594
0.00047128 0.99999983 0.00035362 -0.16354536
0.00050347 -0.00035386 0.99999981 -0.01943440
Axis -0.45639766 -0.64969767 0.60794252
Axis point 75.97965458 -0.00000000 304.52766118
Rotation angle (degrees) 0.04440799
Shift along axis 0.03086114
> fitmap #4.6 inMap #4.9
Fit map pre1_GDP-Pi_EFG.mrc in map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc
using 72149 points
correlation = 0.9999, correlation about mean = 0.9991, overlap = 9.429e+05
steps = 92, shift = 4.77, angle = 3 degrees
Position of pre1_GDP-Pi_EFG.mrc (#4.6) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
0.99999991 0.00004762 -0.00042343 0.04112513
-0.00004771 0.99999997 -0.00022630 0.06814932
0.00042342 0.00022632 0.99999988 -0.11199685
Axis 0.46906646 -0.87762003 -0.09879141
Axis point 271.41553503 0.00000000 129.69563440
Rotation angle (degrees) 0.02764323
Shift along axis -0.02945447
> fitmap #4.7 inMap #4.9
Fit map pre1_GDP-Pi_apra.mrc in map pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc using 1530 points
correlation = 0.996, correlation about mean = 0.972, overlap = 3.929e+04
steps = 56, shift = 1.56, angle = 1.61 degrees
Position of pre1_GDP-Pi_apra.mrc (#4.7) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
0.99964109 0.00848759 0.02540955 -5.64171230
-0.00823457 0.99991563 -0.01004566 3.20970290
-0.02549267 0.00983281 0.99962665 2.66465996
Axis 0.34784583 0.89071874 -0.29261479
Axis point 102.57055802 0.00000000 225.07857793
Rotation angle (degrees) 1.63737420
Shift along axis 0.11677752
> fitmap #4.8 inMap #4.9
Fit map pre1_GDP-Pi_mrna.mrc in map pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc using 5665 points
correlation = 0.9982, correlation about mean = 0.9826, overlap = 1.481e+05
steps = 76, shift = 1.65, angle = 3.47 degrees
Position of pre1_GDP-Pi_mrna.mrc (#4.8) relative to pre1_GDP-
Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates:
Matrix rotation and translation
0.99997555 -0.00275719 -0.00642686 1.70478645
0.00278904 0.99998385 0.00495222 -1.37214422
0.00641310 -0.00497002 0.99996708 -0.27159665
Axis -0.57860172 -0.74874473 0.32342138
Axis point 41.32673193 0.00000000 260.88493337
Rotation angle (degrees) 0.49127847
Shift along axis -0.04684678
> show #!4.8 models
> hide #!4.8 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4 models
> show #!1.1 models
> hide #!5.3 models
> hide #!5.4 models
> hide #!5.5 models
> hide #!5.6 models
> hide #!5.7 models
> hide #!5.8 models
> hide #!5.10 models
> hide #!5.9 models
> show #!5.1 models
> fitmap #5.1 inMap #1.1
Fit map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc in map
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 889296 points
correlation = 0.7608, correlation about mean = 0.356, overlap = 8.617e+06
steps = 200, shift = 0.719, angle = 2.62 degrees
Position of pre2_GDP-Pi_job918_5A_sharpened_b100.mrc (#5.1) relative to
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99927516 0.00172680 -0.03802852 6.04543288
-0.00075966 0.99967627 0.02543193 -4.22182369
0.03806012 -0.02538461 0.99895298 -1.35811292
Axis -0.55518187 -0.83128524 -0.02716510
Axis point 39.97630304 0.00000000 160.98461928
Rotation angle (degrees) 2.62309569
Shift along axis 0.19011823
> fitmap #5.3 inMap #5.1
Fit map pre2_GDP-Pi_head.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 93826 points
correlation = 1, correlation about mean = 0.9994, overlap = 9.106e+05
steps = 72, shift = 3.55, angle = 2.7 degrees
Position of pre2_GDP-Pi_head.mrc (#5.3) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
0.99999892 0.00051730 -0.00137436 0.28373044
-0.00051681 0.99999980 0.00035954 -0.02658987
0.00137455 -0.00035883 0.99999899 -0.17584155
Axis -0.23759161 -0.90916149 -0.34201698
Axis point 123.87461941 0.00000000 209.27025801
Rotation angle (degrees) 0.08661878
Shift along axis 0.01690331
> fitmap #5.4 inMap #5.1
Fit map pre2_GDP-Pi_body.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 212965 points
correlation = 1, correlation about mean = 0.9999, overlap = 2.233e+06
steps = 64, shift = 1.32, angle = 2.63 degrees
Position of pre2_GDP-Pi_body.mrc (#5.4) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
1.00000000 0.00008537 0.00001950 -0.02014495
-0.00008537 0.99999998 0.00015206 -0.01976849
-0.00001949 -0.00015206 0.99999999 0.03978210
Axis -0.86657156 0.11110461 -0.48652800
Axis point -0.00000000 248.50989590 127.03866056
Rotation angle (degrees) 0.01005385
Shift along axis -0.00409443
> fitmap #5.5 inMap #5.1
Fit map pre2_GDP-Pi_LSU.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 555366 points
correlation = 1, correlation about mean = 1, overlap = 6.164e+06
steps = 80, shift = 0.586, angle = 2.62 degrees
Position of pre2_GDP-Pi_LSU.mrc (#5.5) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
1.00000000 0.00004679 0.00000773 -0.01437486
-0.00004679 1.00000000 -0.00004642 0.01041546
-0.00000773 0.00004642 1.00000000 -0.00730890
Axis 0.69947950 0.11647881 -0.70509653
Axis point 231.76331831 252.08005120 0.00000000
Rotation angle (degrees) 0.00380226
Shift along axis -0.00368827
> fitmap #5.6 inMap #5.1
Fit map pre2_GDP-Pi_atrna.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 7392 points
correlation = 0.9985, correlation about mean = 0.9643, overlap = 5.814e+04
steps = 48, shift = 2.2, angle = 2.71 degrees
Position of pre2_GDP-Pi_atrna.mrc (#5.6) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
0.99997110 0.00435468 -0.00623160 0.60271668
-0.00441370 0.99994524 -0.00948900 2.69778464
0.00618994 0.00951623 0.99993556 -2.39843357
Axis 0.78086075 -0.51035936 -0.36026352
Axis point 0.00000000 255.53107136 280.56572185
Rotation angle (degrees) 0.69727299
Shift along axis -0.04213372
> fitmap #5.7 inMap #5.1
Fit map pre2_GDP-Pi_ptrna.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 9819 points
correlation = 0.9998, correlation about mean = 0.9967, overlap = 8.684e+04
steps = 56, shift = 2.43, angle = 2.7 degrees
Position of pre2_GDP-Pi_ptrna.mrc (#5.7) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
0.99999663 -0.00189626 -0.00177369 0.58902917
0.00189572 0.99999816 -0.00030632 -0.24437857
0.00177427 0.00030296 0.99999838 -0.32193593
Axis 0.11652836 -0.67856763 0.72523590
Axis point 128.85957840 310.33743994 0.00000000
Rotation angle (degrees) 0.14978881
Shift along axis 0.00098650
> fitmap #5.8 inMap #5.1
Fit map pre2_GDP-Pi_EFG.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 13847 points
correlation = 0.9999, correlation about mean = 0.9966, overlap = 9.133e+04
steps = 60, shift = 4.14, angle = 2.72 degrees
Position of pre2_GDP-Pi_EFG.mrc (#5.8) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
0.99999603 0.00166220 -0.00227738 0.12036839
-0.00166318 0.99999852 -0.00043071 0.46680606
0.00227667 0.00043450 0.99999731 -0.53839913
Axis 0.15165996 -0.79826752 -0.58289641
Axis point 246.93295335 0.00000000 55.12319995
Rotation angle (degrees) 0.16343406
Shift along axis -0.04055012
> fitmap #5.9 inMap #5.1
Fit map pre2_GDP-Pi_apra.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 233 points
correlation = 0.9958, correlation about mean = 0.8491, overlap = 2534
steps = 44, shift = 1.14, angle = 3.24 degrees
Position of pre2_GDP-Pi_apra.mrc (#5.9) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
0.99635246 -0.01906506 0.08317637 -12.11764764
0.01877923 0.99981476 0.00421751 -3.33803710
-0.08324137 -0.00264013 0.99652592 13.33580403
Axis -0.04014914 0.97431866 0.22156535
Axis point 153.34643675 0.00000000 152.31969587
Rotation angle (degrees) 4.89914817
Shift along axis 0.18895328
> fitmap #5.10 inMap #5.1
Fit map pre2_GDP-Pi_mrna.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc
using 860 points
correlation = 0.9988, correlation about mean = 0.9342, overlap = 1.143e+04
steps = 52, shift = 1.57, angle = 3.42 degrees
Position of pre2_GDP-Pi_mrna.mrc (#5.10) relative to pre2_GDP-
Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates:
Matrix rotation and translation
0.99978500 -0.02018208 0.00475772 1.88844381
0.02007967 0.99958468 0.02067083 -6.68983380
-0.00517292 -0.02057085 0.99977502 3.54784779
Axis -0.70516611 0.16979791 0.68841080
Axis point 0.00000000 169.73864150 326.83981200
Rotation angle (degrees) 1.67571236
Shift along axis -0.02520962
> show #!5.3 models
> show #!5.4 models
> show #!5.5 models
> hide #!5.5 models
> hide #!5.4 models
> hide #!5.3 models
> hide #!5.1 models
> hide #!5 models
> fitmap #6 inMap #1.1
Fit map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc in map
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 2582330 points
correlation = 0.8915, correlation about mean = 0.5999, overlap = 5.811e+07
steps = 180, shift = 0.747, angle = 4.9 degrees
Position of chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) relative to
70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99673555 0.04201445 -0.06894226 4.97827100
-0.04008241 0.99877042 0.02917258 1.73392276
0.07008316 -0.02631397 0.99719403 -6.37784818
Axis -0.32500711 -0.81432804 -0.48087443
Axis point 93.47108066 0.00000000 67.95774460
Rotation angle (degrees) 4.89684458
Shift along axis 0.03698874
> show #!6 models
> hide #!1.1 models
> show #7 models
> hide #!6 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> fitmap #8 inMap #6
Fit map chimeric_GDP1_head.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 153790 points
correlation = 0.9999, correlation about mean = 0.9998, overlap = 8.809e+05
steps = 100, shift = 8.22, angle = 4.93 degrees
Position of chimeric_GDP1_head.mrc (#8) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
0.99999982 0.00002670 -0.00059450 0.14477295
-0.00002658 0.99999998 0.00021029 -0.04663208
0.00059450 -0.00021027 0.99999980 -0.07365861
Axis -0.33316354 -0.94192378 -0.04220958
Axis point 124.06592046 0.00000000 242.81214249
Rotation angle (degrees) 0.03616253
Shift along axis -0.00120011
> fitmap #9 inMap #6
Fit map chimeric_GDP1_body.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 167699 points
correlation = 1, correlation about mean = 1, overlap = 2.052e+06
steps = 100, shift = 0.9, angle = 4.89 degrees
Position of chimeric_GDP1_body.mrc (#9) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
1.00000000 -0.00002372 0.00005887 -0.00551886
0.00002372 1.00000000 0.00005608 -0.01289350
-0.00005887 -0.00005608 1.00000000 0.02325899
Axis -0.66214550 0.69508141 0.28004495
Axis point 389.33106877 0.00000000 80.19525840
Rotation angle (degrees) 0.00485286
Shift along axis 0.00120582
> fitmap #10 inMap #6
Fit map chimeric_GDP1_LSU.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 167597 points
correlation = 1, correlation about mean = 1, overlap = 5.139e+06
steps = 120, shift = 2.22, angle = 4.9 degrees
Position of chimeric_GDP1_LSU.mrc (#10) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
1.00000000 0.00005749 0.00002314 -0.01671964
-0.00005749 1.00000000 -0.00005001 0.01924092
-0.00002314 0.00005001 1.00000000 -0.00364929
Axis 0.62799409 0.29061433 -0.72191878
Axis point 346.16272008 265.99659198 0.00000000
Rotation angle (degrees) 0.00456280
Shift along axis -0.00227366
> fitmap #11 inMap #6
Fit map chimeric_GDP1_atrna.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 16417 points
correlation = 0.9981, correlation about mean = 0.9951, overlap = 6.038e+04
steps = 80, shift = 3.41, angle = 4.95 degrees
Position of chimeric_GDP1_atrna.mrc (#11) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
0.99999756 0.00004752 -0.00220774 0.46424097
-0.00005368 0.99999610 -0.00279156 0.59428195
0.00220760 0.00279168 0.99999367 -0.81073365
Axis 0.78429009 -0.62023136 -0.01421658
Axis point 0.00000000 290.86084881 214.04141267
Rotation angle (degrees) 0.20394035
Shift along axis 0.00703315
> fitmap #12 inMap #6
Fit map chimeric_GDP1_ptrna.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 17350 points
correlation = 0.9991, correlation about mean = 0.9978, overlap = 9.266e+04
steps = 96, shift = 4.32, angle = 4.88 degrees
Position of chimeric_GDP1_ptrna.mrc (#12) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
0.99999912 -0.00131485 -0.00018403 0.19658134
0.00131495 0.99999901 0.00050208 -0.32974506
0.00018337 -0.00050232 0.99999986 0.08526727
Axis -0.35379255 -0.12941147 0.92632797
Axis point 245.76146418 163.36447906 0.00000000
Rotation angle (degrees) 0.08133006
Shift along axis 0.05210924
> fitmap #13 inMap #6
Fit map chimeric_GDP1_EFG.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 50191 points
correlation = 1, correlation about mean = 0.9999, overlap = 1.808e+05
steps = 96, shift = 5.46, angle = 4.89 degrees
Position of chimeric_GDP1_EFG.mrc (#13) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
1.00000000 -0.00007450 -0.00000784 0.00431330
0.00007449 0.99999996 -0.00028369 0.04169017
0.00000786 0.00028369 0.99999996 -0.03220365
Axis 0.96686348 -0.02675683 0.25388794
Axis point 0.00000000 108.95423277 146.45648771
Rotation angle (degrees) 0.01681138
Shift along axis -0.00512124
> fitmap #14 inMap #6
Fit map chimeric_GDP1_apra.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 555 points
correlation = 0.9897, correlation about mean = 0.978, overlap = 4553
steps = 64, shift = 3.09, angle = 5.26 degrees
Position of chimeric_GDP1_apra.mrc (#14) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
0.99972466 0.02147684 0.00945209 -4.39025179
-0.02149551 0.99976718 0.00187810 3.23895043
-0.00940956 -0.00208076 0.99995356 1.67873632
Axis -0.08405903 0.40049152 -0.91243664
Axis point 145.94628769 205.76268949 -0.00000000
Rotation angle (degrees) 1.34933314
Shift along axis 0.13447195
> fitmap #15 inMap #6
Fit map chimeric_GDP1_mrna.mrc in map
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 2808 points
correlation = 0.9945, correlation about mean = 0.9862, overlap = 1.156e+04
steps = 100, shift = 4.32, angle = 5.06 degrees
Position of chimeric_GDP1_mrna.mrc (#15) relative to
chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates:
Matrix rotation and translation
0.99998260 0.00573335 0.00138856 -0.94639803
-0.00573756 0.99997890 0.00304728 0.24427763
-0.00137106 -0.00305519 0.99999439 0.73376284
Axis -0.45942034 0.20775636 -0.86357990
Axis point 47.28720648 177.08135346 0.00000000
Rotation angle (degrees) 0.38053196
Shift along axis -0.14811811
> show #!6 models
> hide #7 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> volume #8 step 1
> volume #9 step 1
> volume #10 step 1
> volume #11 step 1
> volume #12 step 1
> volume #13 step 1
> volume #14 step 1
> volume #15 step 1
> hide #!9 models
> hide #!6 models
> show #!9 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!12 models
> show #!11 models
> show #!10 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 2
> volume #8 level 2.5
> volume #9 level 2.5
> volume #10 level 2.5
> volume #11 level 2
> volume #12 level 2
> volume #13 level 2.5
> volume #14 level 2.5
> volume #15 level 3
> surface dust #8 size 5
> surface dust #9 size 5
> surface dust #10 size 5
> surface dust #11 size 5
> surface dust #12 size 5
> surface dust #13 size 5
> surface dust #13 size 5view 2
Invalid "size" argument: Expected a number
> view 2
> rename #6-15 id #16
> rename #16 Chimeric_GDP1
> rename #16 id #6
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2
> -Stark/temporary/Figures_paper_20201130/all_states-session-4.cxs"
> includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
540, in compress
f.write(data)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
280, in write
self.fileobj.write(self.compress.compress(data))
MemoryError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\map\session.py", line 311, in state_from_grid_data
s['array'] = b64encode(compress(dt.matrix().tobytes()))
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
540, in compress
f.write(data)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
325, in close
fileobj.write(self.compress.flush())
ValueError: I/O operation on closed file.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BC956084C0> ->
<chimerax.std_commands.view.NamedView object at 0x000001BC95608EE0> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BC8B082A30> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BC8B3BA8E0>
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BD3F59E100>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BC956084C0> ->
<chimerax.std_commands.view.NamedView object at 0x000001BC95608EE0> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BC8B082A30> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BC8B3BA8E0>
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BD3F59E100>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BC956084C0> ->
<chimerax.std_commands.view.NamedView object at 0x000001BC95608EE0> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BC8B082A30> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BC8B3BA8E0>
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BD3F59E100>
ValueError: error processing: 'named views' -> -> -> 'surface' ->
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> : Error while saving session
data for 'named views' -> -> -> 'surface' ->
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
540, in compress
f.write(data)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
280, in write
self.fileobj.write(self.compress.compress(data))
MemoryError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\map\session.py", line 311, in state_from_grid_data
s['array'] = b64encode(compress(dt.matrix().tobytes()))
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
540, in compress
f.write(data)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py", line
325, in close
fileobj.write(self.compress.flush())
ValueError: I/O operation on closed file.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BC956084C0> ->
<chimerax.std_commands.view.NamedView object at 0x000001BC95608EE0> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BC8B082A30> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BC8B3BA8E0>
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BD3F59E100>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\ui\gui.py", line 1601, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 78, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BC956084C0> ->
<chimerax.std_commands.view.NamedView object at 0x000001BC95608EE0> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BC8B082A30> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BC8B3BA8E0>
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BD3F59E100>: Error while
saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x000001BC956084C0> ->
<chimerax.std_commands.view.NamedView object at 0x000001BC95608EE0> ->
<chimerax.map.volume.VolumeSurface object at 0x000001BC8B082A30> 'surface' ->
<chimerax.map.volume.Volume object at 0x000001BC8B3BA8E0>
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
<chimerax.map.session.GridDataState object at 0x000001BD3F59E100>
ValueError: error processing: 'named views' -> -> -> 'surface' ->
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> : Error while saving session
data for 'named views' -> -> -> 'surface' ->
'70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' ->
File "C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 442.94
OpenGL renderer: GeForce MX250/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ZenBook UX463FL_UX463FL
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 8,356,536,320
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
OSLanguage: en-GB
Locale: ('en_DE', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.11.8
cftime: 1.3.0
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: 1.9.4
ChimeraX-AtomicLibrary: 1.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.2
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: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202011201839
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0.1
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: 2.1
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.1
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: 1.3.1
ChimeraX-PDB: 2.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.2.2
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: 1.3.1
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: 0.29.21
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: 0.17
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.0
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.5.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.1
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.2.3
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.8
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.1
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.1
python-dateutil: 2.8.1
pytz: 2020.4
pywin32: 228
pyzmq: 20.0.0
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.0
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.35.1
WMI: 1.5.1
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError writing compressed session |
comment:2 by , 5 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
The ChimeraX error messages you ran out of memory saving a session. It was trying to include maps in the session because you used the includeMaps true option. This requires reading the full resolution maps into memory and compressing them and that is when it ran out of memory. Your machine has only 8 Gbytes of memory and that is not enough to handle large data sets. You can leave out the "includeMaps true" option and then it will not use so much memory, but then of course the maps will not be put into the session file, instead paths to where the maps are on disk will be put in the session file. Later if those map files move or are deleted the session will not be able to open the map data, so the session files are not self-contained.
You reported bugs before which were the same problem out-of-memory on a machine with only 8 Gbytes and large data sets. Memory is cheap, maybe $100-200 to make the computer more usable on larger data. Some laptops cannot add memory and I don't know about your ASUS ZenBook.
follow-up: 3 comment:3 by , 5 years ago
Ok, thank you for the feedback! On Mon, 30 Nov 2020 at 20:36, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
Note:
See TracTickets
for help on using tickets.
Reported by Ana Schwarzer