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Opened 5 years ago
Closed 5 years ago
#3816 closed defect (not a bug)
Unable to allocate buffer
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/ChimeraX_sessions/Wild-
> type_partial_20201011.cxs"
Log from Sun Oct 11 13:29:14 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/ChimeraX_sessions/Wild-
> type_partial_20201010.cxs"
Log from Sat Oct 10 23:03:59 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_sessions/Pre0-Pre1_p610l.cxs"
Log from Sat Oct 10 20:55:35 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G3/ChimeraX_sessions/Pre0-Pre1-Pre2_20201010.cxs"
Log from Sat Oct 10 17:06:49 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/EF-G_WT_states_20201010.cxs"
Log from Sat Oct 10 16:21:08 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/70S_AP_v2.cif-coot-2.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/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 #1
---
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
> select /w:1-76
1631 atoms, 1821 bonds, 1 model selected
> ui mousemode right select
> select clear
> ui mousemode right translate
> select /0:1-56
444 atoms, 450 bonds, 1 model selected
> select /B:1-120
2570 atoms, 2873 bonds, 1 model selected
> select #1/0-6
3208 atoms, 3239 bonds, 1 model selected
> select #1/0-6,A-Z
92129 atoms, 99979 bonds, 1 model selected
> cd
Current working directory is: C:\Users\anasc
> save Pre0_wt_30S.pdb selectedOnly true
> ui mousemode right select
> select clear
> ui mousemode right translate
> select #1/a-u,x-z
52207 atoms, 56371 bonds, 1 model selected
> save Pre0_wt_50S.pdb selectedOnly true
> select #1/v
1642 atoms, 1834 bonds, 1 model selected
> save Pre0_wt_ptRNA.pdb selectedOnly true
> select #1/w
1631 atoms, 1821 bonds, 1 model selected
> save Pre0_wt_atRNA.pdb selectedOnly true
> ui mousemode right select
> select clear
> ui mousemode right translate
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/pre0_j536_3d512_235A_sharpened.mrc"
Opened pre0_j536_3d512_235A_sharpened.mrc, grid size 512,512,512, pixel 0.652,
shown at level 5.08, step 2, values float32
> volume #2 step 1
> volume #2 level 3
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre0/Pre0_wt_30S.pdb
---
warnings | Ignored bad PDB record found on line 53203
END
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
245 messages similar to the above omitted
Chain information for Pre0_wt_30S.pdb #3
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre0/Pre0_wt_50S.pdb
---
warnings | Ignored bad PDB record found on line 94314
END
Start residue of secondary structure not found: HELIX 116 116 THR b 19 TYR b
21 1 3
Start residue of secondary structure not found: HELIX 117 117 PRO b 24 PHE b
29 1 6
Start residue of secondary structure not found: HELIX 118 118 LEU b 42 SER b
61 1 20
Start residue of secondary structure not found: HELIX 119 119 ARG b 73 SER b
85 1 13
Start residue of secondary structure not found: HELIX 120 120 TRP b 103 GLN b
121 1 19
156 messages similar to the above omitted
Chain information for Pre0_wt_50S.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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre0/Pre0_wt_atRNA.pdb
---
warnings | Ignored bad PDB record found on line 2231
END
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
406 messages similar to the above omitted
Chain information for Pre0_wt_atRNA.pdb #5
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre0/Pre0_wt_ptRNA.pdb
---
warnings | Ignored bad PDB record found on line 2202
END
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
406 messages similar to the above omitted
Chain information for Pre0_wt_ptRNA.pdb #6
---
Chain | Description
v | No description available
Must specify one map, got 0
> fitmap #3 inMap #2 resolution 2.3 metric correlation
Fit map Pre0_wt_30S.pdb map 2.3 in map pre0_j536_3d512_235A_sharpened.mrc
using 765126 points
correlation = 0.8168, correlation about mean = 0.4404, overlap = 3.908e+06
steps = 48, shift = 0.00864, angle = 0.00819 degrees
Position of Pre0_wt_30S.pdb map 2.3 (#7) relative to
pre0_j536_3d512_235A_sharpened.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000553 0.00008725 -0.00928155
-0.00000552 0.99999999 -0.00011315 0.02271066
-0.00008725 0.00011315 0.99999999 -0.00581553
Axis 0.79131275 0.61018979 -0.03863360
Axis point 0.00000000 49.10917451 164.36782572
Rotation angle (degrees) 0.00819304
Shift along axis 0.00673788
> fitmap #4 inMap #2 resolution 2.3 metric correlation
Fit map Pre0_wt_50S.pdb map 2.3 in map pre0_j536_3d512_235A_sharpened.mrc
using 1350493 points
correlation = 0.8207, correlation about mean = 0.4682, overlap = 7.57e+06
steps = 48, shift = 0.00468, angle = 0.00337 degrees
Position of Pre0_wt_50S.pdb map 2.3 (#8) relative to
pre0_j536_3d512_235A_sharpened.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00005377 -0.00001036 -0.00961917
-0.00005377 1.00000000 0.00002144 0.01014318
0.00001037 -0.00002144 1.00000000 0.00501730
Axis -0.36461384 -0.17625433 -0.91432552
Axis point 179.24450263 198.35905366 0.00000000
Rotation angle (degrees) 0.00336926
Shift along axis -0.00286795
> fitmap #5 inMap #2 resolution 2.3 metric correlation
Fit map Pre0_wt_atRNA.pdb map 2.3 in map pre0_j536_3d512_235A_sharpened.mrc
using 23495 points
correlation = 0.7761, correlation about mean = 0.2844, overlap = 9.644e+04
steps = 40, shift = 0.0283, angle = 0.0977 degrees
Position of Pre0_wt_atRNA.pdb map 2.3 (#9) relative to
pre0_j536_3d512_235A_sharpened.mrc (#2) coordinates:
Matrix rotation and translation
0.99999980 0.00055611 -0.00030951 -0.01014574
-0.00055561 0.99999859 0.00158184 -0.21749285
0.00031039 -0.00158167 0.99999870 0.13354832
Axis -0.92772036 -0.18178772 -0.32601866
Axis point 0.00000000 85.43771064 136.94734241
Rotation angle (degrees) 0.09768902
Shift along axis 0.00541070
> fitmap #6 inMap #2 resolution 2.3 metric correlation
Fit map Pre0_wt_ptRNA.pdb map 2.3 in map pre0_j536_3d512_235A_sharpened.mrc
using 23655 points
correlation = 0.7853, correlation about mean = 0.3395, overlap = 1.06e+05
steps = 44, shift = 0.0241, angle = 0.132 degrees
Position of Pre0_wt_ptRNA.pdb map 2.3 (#10) relative to
pre0_j536_3d512_235A_sharpened.mrc (#2) coordinates:
Matrix rotation and translation
0.99999760 0.00171573 0.00136340 -0.54599369
-0.00171475 0.99999827 -0.00071978 0.41525471
-0.00136463 0.00071744 0.99999881 0.12333939
Axis 0.31158708 0.59142995 -0.74372313
Axis point 247.45590603 315.62064041 -0.00000000
Rotation angle (degrees) 0.13214105
Shift along axis -0.01626087
> hide #1 models
> show #!7 models
> hide #!7 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!2 models
> select #7-10
8 models selected
> volume sel level 0.02
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> set bgColor white
> graphics silhouettes true
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> lighting full
> lighting simple
> view name 1
> color #9 light sky blue
> color #10 blue
> show #!2 models
> hide #!2 models
> show #1 models
> view 1
> hide #1 models
> save Pre0_wt_30S.mrc models #7
> save Pre0_wt_50S.mrc models #8
> save Pre0_wt_atRNA.mrc models #9
> save Pre0_wt_ptRNA.mrc models #10
> save C:\Users\anasc\Desktop\image1.png supersample 3
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/70S_tRNA_c1_real_space_refined.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models
Valik/70S_tRNA_c1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 3090
TER
Ignored bad PDB record found on line 3501
TER
Ignored bad PDB record found on line 3879
TER
Ignored bad PDB record found on line 4384
TER
Ignored bad PDB record found on line 4687
TER
54 messages similar to the above omitted
Chain information for 70S_tRNA_c1_real_space_refined.pdb #11
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/pre1_j620_3d288_44A_sharpened.mrc"
Opened pre1_j620_3d288_44A_sharpened.mrc, grid size 288,288,288, pixel 1.16,
shown at level 4, step 2, values float32
> volume #12 step 1
> volume #12 level 3
> hide #!12 models
> select #11/0-6,A-Z
92140 atoms, 99978 bonds, 433 pseudobonds, 2 models selected
> save Pre1_wt_30S.pdb selectedOnly true
> select #1/a-u,x-z
52207 atoms, 56371 bonds, 1 model selected
> select #11/a-u,x-z
52213 atoms, 56371 bonds, 176 pseudobonds, 2 models selected
> save Pre1_wt_30S_.pdb selectedOnly true
> select #11/v
1643 atoms, 1834 bonds, 1 model selected
> save Pre1_wt_ptRNA.pdb selectedOnly true
> select #11/w
1637 atoms, 1821 bonds, 1 model selected
> save Pre1_wt_atRNA.pdb selectedOnly true
> hide #!11 models
> show #!12 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1/Pre1_wt_50S.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
1 messages similar to the above omitted
Chain information for Pre1_wt_50S.pdb #13
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1/Pre1_wt_30S.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
1 messages similar to the above omitted
Chain information for Pre1_wt_30S.pdb #14
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1/Pre1_wt_ptRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
1 messages similar to the above omitted
Chain information for Pre1_wt_ptRNA.pdb #15
---
Chain | Description
v | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1/Pre1_wt_atRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
1 messages similar to the above omitted
Chain information for Pre1_wt_atRNA.pdb #16
---
Chain | Description
w | No description available
> fitmap #13 inMap #12 resolution 4.4 metric correlation
Fit map Pre1_wt_50S.pdb map 4.4 in map pre1_j620_3d288_44A_sharpened.mrc using
409299 points
correlation = 0.8518, correlation about mean = 0.5672, overlap = 5.642e+05
steps = 40, shift = 0.0426, angle = 0.0364 degrees
Position of Pre1_wt_50S.pdb map 4.4 (#17) relative to
pre1_j620_3d288_44A_sharpened.mrc (#12) coordinates:
Matrix rotation and translation
0.99999991 0.00043167 0.00000474 -0.06940873
-0.00043167 0.99999980 0.00046541 -0.03400786
-0.00000454 -0.00046541 0.99999989 0.10157547
Axis -0.73316509 0.00731488 -0.68001135
Axis point 0.00000000 191.29852390 72.86371248
Rotation angle (degrees) 0.03637126
Shift along axis -0.01843318
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #14 inMap #12 resolution 4.4 metric correlation
Fit map Pre1_wt_30S.pdb map 4.4 in map pre1_j620_3d288_44A_sharpened.mrc using
234615 points
correlation = 0.855, correlation about mean = 0.5312, overlap = 2.81e+05
steps = 48, shift = 0.0381, angle = 0.0854 degrees
Position of Pre1_wt_30S.pdb map 4.4 (#18) relative to
pre1_j620_3d288_44A_sharpened.mrc (#12) coordinates:
Matrix rotation and translation
0.99999927 0.00027786 0.00117278 -0.20997101
-0.00027683 0.99999958 -0.00087566 0.19171440
-0.00117303 0.00087533 0.99999893 0.03294396
Axis 0.58770988 0.78735956 -0.18617742
Axis point 31.30980829 0.00000000 189.78621940
Rotation angle (degrees) 0.08535179
Shift along axis 0.02141271
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #15 inMap #12 resolution 4.4 metric correlation
Fit map Pre1_wt_ptRNA.pdb map 4.4 in map pre1_j620_3d288_44A_sharpened.mrc
using 7245 points
correlation = 0.8413, correlation about mean = 0.4575, overlap = 8023
steps = 44, shift = 0.102, angle = 0.177 degrees
Position of Pre1_wt_ptRNA.pdb map 4.4 (#19) relative to
pre1_j620_3d288_44A_sharpened.mrc (#12) coordinates:
Matrix rotation and translation
0.99999530 -0.00214555 0.00218879 -0.18810789
0.00214638 0.99999763 -0.00037585 -0.29114775
-0.00218798 0.00038054 0.99999753 0.21568078
Axis 0.12246318 0.70861968 0.69488195
Axis point 123.72412800 0.00000000 81.76017967
Rotation angle (degrees) 0.17694333
Shift along axis -0.07947664
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #16 inMap #12 resolution 4.4 metric correlation
Fit map Pre1_wt_atRNA.pdb map 4.4 in map pre1_j620_3d288_44A_sharpened.mrc
using 7213 points
correlation = 0.8202, correlation about mean = 0.3725, overlap = 7190
steps = 48, shift = 0.161, angle = 0.122 degrees
Position of Pre1_wt_atRNA.pdb map 4.4 (#20) relative to
pre1_j620_3d288_44A_sharpened.mrc (#12) coordinates:
Matrix rotation and translation
0.99999874 -0.00140561 -0.00073879 0.17965033
0.00140456 0.99999800 -0.00142332 -0.00717316
0.00074079 0.00142228 0.99999871 -0.29920166
Axis 0.66731907 -0.34697276 0.65901075
Axis point 0.00000000 175.68586416 -23.52204043
Rotation angle (degrees) 0.12216127
Shift along axis -0.07480413
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> save Pre1_wt_50S.mrc models #17
> save Pre1_wt_30S.mrc models #18
> save Pre1_wt_ptRNA.mrc models #19
> save Pre1_wt_atRNA.mrc models #20
> hide #!13 models
> hide #!14 models
> hide #15 models
> hide #16 models
> hide #!12 models
> show #!17 models
> show #!18 models
> show #!19 models
> show #!20 models
> color #19 light sky blue
> color #20 light sky blue
> color #19 blue
> view 1
> select #17-20
8 models selected
> volume sel level 0.02
> ui mousemode right select
> select clear
> ui mousemode right translate
> save C:\Users\anasc\Desktop\image1.png supersample 3
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/70S_tRNA_c2_real_space_refined.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models
Valik/Pre2/70S_tRNA_c2_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 3092
TER
Ignored bad PDB record found on line 3503
TER
Ignored bad PDB record found on line 3881
TER
Ignored bad PDB record found on line 4386
TER
Ignored bad PDB record found on line 4689
TER
54 messages similar to the above omitted
Chain information for 70S_tRNA_c2_real_space_refined.pdb #21
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/pre2_j621_3d288_95A_sharpened.mrc"
Opened pre2_j621_3d288_95A_sharpened.mrc, grid size 288,288,288, pixel 1.16,
shown at level 4.17, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #21/0-6,A-Z
92140 atoms, 99979 bonds, 433 pseudobonds, 2 models selected
> save Pre2_wt_50S.pdb selectedOnly true
> select #1/a-u,x-z
52207 atoms, 56371 bonds, 1 model selected
> select #12/a-u,x-z
Nothing selected
> select #21/a-u,x-z
52213 atoms, 56371 bonds, 176 pseudobonds, 2 models selected
> save Pre2_wt_30S.pdb selectedOnly true
> select #21/v
1643 atoms, 1834 bonds, 1 model selected
> save Pre2_wt_ptRNA.pdb selectedOnly true
> select #1/w
1631 atoms, 1821 bonds, 1 model selected
> select #21/w
1637 atoms, 1821 bonds, 1 model selected
> save Pre2_wt_atRNA.pdb selectedOnly true
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2/Pre2_wt_50S.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
6 messages similar to the above omitted
Chain information for Pre2_wt_50S.pdb #23
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2/Pre2_wt_30S.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
6 messages similar to the above omitted
Chain information for Pre2_wt_30S.pdb #24
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2/Pre2_wt_atRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
6 messages similar to the above omitted
Chain information for Pre2_wt_atRNA.pdb #25
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2/Pre2_wt_ptRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
6 messages similar to the above omitted
Chain information for Pre2_wt_ptRNA.pdb #26
---
Chain | Description
v | No description available
> hide #!21 models
> hide #!22 models
> show #!22 models
> fitmap #23 inMap #22 resolution 9.5 metric correlation
Fit map Pre2_wt_50S.pdb map 9.5 in map pre2_j621_3d288_95A_sharpened.mrc using
63259 points
correlation = 0.9028, correlation about mean = 0.7859, overlap = 5.144e+04
steps = 40, shift = 0.0531, angle = 0.0826 degrees
Position of Pre2_wt_50S.pdb map 9.5 (#27) relative to
pre2_j621_3d288_95A_sharpened.mrc (#22) coordinates:
Matrix rotation and translation
0.99999897 0.00125354 0.00069355 -0.32390632
-0.00125342 0.99999920 -0.00016583 0.25396073
-0.00069376 0.00016496 0.99999975 0.13777795
Axis 0.11468941 0.48099513 -0.86918929
Axis point 215.78596229 255.39101667 0.00000000
Rotation angle (degrees) 0.08262776
Shift along axis -0.03474988
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #24 inMap #22 resolution 9.5 metric correlation
Fit map Pre2_wt_30S.pdb map 9.5 in map pre2_j621_3d288_95A_sharpened.mrc using
36606 points
correlation = 0.9075, correlation about mean = 0.7788, overlap = 2.745e+04
steps = 60, shift = 0.0932, angle = 0.167 degrees
Position of Pre2_wt_30S.pdb map 9.5 (#28) relative to
pre2_j621_3d288_95A_sharpened.mrc (#22) coordinates:
Matrix rotation and translation
0.99999743 0.00141868 0.00176986 -0.55737880
-0.00141543 0.99999731 -0.00183632 0.50776139
-0.00177246 0.00183381 0.99999675 0.00173245
Axis 0.62895891 0.60705662 -0.48568811
Axis point 0.00000000 11.00457975 290.76571056
Rotation angle (degrees) 0.16716757
Shift along axis -0.04316988
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #25 inMap #22 resolution 9.5 metric correlation
Fit map Pre2_wt_atRNA.pdb map 9.5 in map pre2_j621_3d288_95A_sharpened.mrc
using 1389 points
correlation = 0.8723, correlation about mean = 0.7336, overlap = 767.7
steps = 60, shift = 0.192, angle = 0.429 degrees
Position of Pre2_wt_atRNA.pdb map 9.5 (#29) relative to
pre2_j621_3d288_95A_sharpened.mrc (#22) coordinates:
Matrix rotation and translation
0.99997319 -0.00136575 0.00719412 -1.40535002
0.00137673 0.99999790 -0.00152074 0.02399398
-0.00719203 0.00153061 0.99997297 1.01845089
Axis 0.20397124 0.96165899 0.18332408
Axis point 142.83957949 0.00000000 193.69984350
Rotation angle (degrees) 0.42856848
Shift along axis -0.07687039
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #26 inMap #22 resolution 9.5 metric correlation
Fit map Pre2_wt_ptRNA.pdb map 9.5 in map pre2_j621_3d288_95A_sharpened.mrc
using 1382 points
correlation = 0.8805, correlation about mean = 0.7216, overlap = 830.5
steps = 48, shift = 0.176, angle = 0.226 degrees
Position of Pre2_wt_ptRNA.pdb map 9.5 (#30) relative to
pre2_j621_3d288_95A_sharpened.mrc (#22) coordinates:
Matrix rotation and translation
0.99999238 0.00156113 -0.00357905 0.37194016
-0.00156313 0.99999862 -0.00055853 0.37814646
0.00357817 0.00056412 0.99999344 -0.52752623
Axis 0.14229252 -0.90716166 -0.39599312
Axis point 156.61327629 0.00000000 106.81696389
Rotation angle (degrees) 0.22602342
Shift along axis -0.08121891
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> hide #26 models
> hide #25 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> color #29 light sky blue
> color #30 blue
> show #!29 models
> show #!30 models
> hide #!30 models
> hide #!29 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> view 1
> save C:\Users\anasc\Desktop\image1.png supersample 3
> save Pre2_wt_50S.mrc models #27
> save Pre2_wt_30S.mrc models #28
Cannot determine format for 'Pre2_wt_atRNAmrc'
> save Pre2_wt_atRNA.mrc models #29
> save Pre2_wt_ptRNA.mrc models #30
> hide #!27 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> show #!2 models
> hide #!2 models
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/EF-G_WT_states_20201010.cxs" includeMaps true
> select #3
52207 atoms, 56371 bonds, 1 model selected
> show #3 models
> volume zone #2 nearAtoms sel range 4
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> show #!2 models
> hide #3 models
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> show #!7 models
> hide #!2 models
> show #!2 models
> hide #!7 models
> volume unzone #2
> show #3 models
> hide #3 models
> show #6 models
> hide #6 models
> show #!7 models
> hide #!2 models
> show #6 models
> hide #6 models
> show #!8 models
> show #5 models
> show #6 models
> select #5-6
3273 atoms, 3655 bonds, 2 models selected
> volume zone #2 nearAtoms sel range 4
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> select clear
> ui mousemode right translate
> show #!2 models
> volume unzone #2
> hide #!2 models
> select #3
52207 atoms, 56371 bonds, 1 model selected
> show #3 models
> hide #5 models
> hide #6 models
> hide #!7 models
> hide #!8 models
> select up
885750 atoms, 960032 bonds, 45 models selected
> select #3
52207 atoms, 56371 bonds, 1 model selected
> volume zone #2 nearAtoms sel range 4 newMap true
> hide #3 models
> show #!7 models
> hide #!7 models
> close #7
> save Pre0_wt_30S.mrc models #31
> rename #31 id #7
> close #8-10
> select #4
92129 atoms, 99979 bonds, 1 model selected
> show #4 models
> volume zone #2 nearAtoms sel range 4 newMap true
> save Pre0_wt_50S.mrc models #8
> hide #4 models
> select #5
1631 atoms, 1821 bonds, 1 model selected
> volume zone #2 nearAtoms sel range 4 newMap true
> select #6
1642 atoms, 1834 bonds, 1 model selected
> volume zone #2 nearAtoms sel range 4 newMap true
> save Pre0_wt_atRNA.mrc models #9
> save Pre0_wt_ptRNA.mrc models #10
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!8 models
> select #7-8
4 models selected
> graphics silhouettes false
> ui mousemode right select
> select clear
> select clear
> select clear
> ui mousemode right translate
> ui mousemode right translate
> show #!9 models
> show #!10 models
> select #9-10
4 models selected
> graphics silhouettes true
> graphics silhouettes false
> ui mousemode right select
> select clear
> select clear
> ui mousemode right translate
> color #9 light sky blue
> color #10 blue
> show #5 models
> show #6 models
> hide #5 models
> view 1
> hide #6 models
> color #5 light sky blue
> color #6 blue
> show #6 models
> show #5 models
> select #5-6
3273 atoms, 3655 bonds, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 3273 atom styles
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> transparency #9 60
> transparency #9 50
> transparency #10 50
> transparency #10 80
> transparency #10 30
> transparency #10 10
> transparency #10 0
> transparency #9 0
> transparency #9 10
> transparency #9 0
> transparency #10 0
> hide #6 models
> hide #5 models
> view 1
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> view1
Unknown command: view1
> view 1
> save C:\Users\anasc\Desktop\image1.png supersample 3
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!12 models
> select #13
92140 atoms, 99978 bonds, 433 pseudobonds, 2 models selected
> show #!13 models
> hide #!12 models
> volume zone #12 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> close #17-20
> save Pre1_wt_50S.mrc models #31
> rename #31 id #17
> select #14
52213 atoms, 56371 bonds, 176 pseudobonds, 2 models selected
> hide #!13 models
> volume zone #12 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #15
1643 atoms, 1834 bonds, 1 model selected
> volume zone #12 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #16
1637 atoms, 1821 bonds, 1 model selected
> volume zone #12 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> save Pre1_wt_30S.mrc models #18
> save Pre1_wt_atRNAS.mrc models #19
> save Pre1_wt_ptRNA.mrc models #19
> save Pre1_wt_atRNA.mrc models #20
> color #19 blue
> color #20 light sky blue
> color #16 light sky blue
> color #15 blue
> view 1
> save C:\Users\anasc\Desktop\image1.png supersample 3
> close #27-30
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> show #!22 models
> select #23
92140 atoms, 99979 bonds, 433 pseudobonds, 2 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #24
52213 atoms, 56371 bonds, 176 pseudobonds, 2 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #25
1637 atoms, 1821 bonds, 1 model selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> volume #27 step 1
> volume #27 level 3
> close #27-29
> show #!22 models
> hide #!22 models
> show #!22 models
> select #22
2 models selected
> volume sel step 1
> volume sel level 3
> select #23
92140 atoms, 99979 bonds, 433 pseudobonds, 2 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #24
52213 atoms, 56371 bonds, 176 pseudobonds, 2 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #25
1637 atoms, 1821 bonds, 1 model selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #26
1643 atoms, 1834 bonds, 1 model selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> save Pre2_wt_50S.mrc models #27
> save Pre2_wt_30S.mrc models #28
> save Pre2_wt_atRNA.mrc models #29
> save Pre2_wt_ptRNA.mrc models #30
> color #29 light sky blue
> color #30 blue
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> show #1 models
> show #!9 models
> show #!10 models
> select #1/z
230 atoms, 255 bonds, 1 model selected
> save Pre0_wt_mRNA.pdb selectedOnly true
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre0/Pre0_wt_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 664
END
Ignored bad PDB record found on line 667
END
Ignored bad PDB record found on line 670
END
Ignored bad PDB record found on line 673
END
Ignored bad PDB record found on line 676
END
10 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
406 messages similar to the above omitted
Chain information for Pre0_wt_mRNA.pdb #31
---
Chain | Description
z | No description available
> volume zone #2 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> hide #1 models
> hide #31 models
> color #32 green
> color #5 deep sky blue
> show #31 models
> color #9 deep sky blue
> color #9 light blue
> color #10 deep sky blue
> show #!7 models
> show #!8 models
> color #9 light blue
> color #10 light blue
> color #9 deep sky blue
> hide #!8 models
> hide #!7 models
> save C:\Users\anasc\Desktop\image1.png supersample 3
> select #31
230 atoms, 255 bonds, 1 model selected
> volume zone #2 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> close #9-10
> select #5
1631 atoms, 1821 bonds, 1 model selected
> volume zone #2 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #6
1642 atoms, 1834 bonds, 1 model selected
> volume zone #2 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> save C:\Users\anasc\Desktop\image2.png supersample 3
> close #17-20
> close #27-30
> show #!7 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> color #5 deep sky blue
> color #6 light blue
> save Pre0_wt_30S_range4.mrc models #7
> save Pre0_wt_50S_range4.mrc models #8
> color #9 deep sky blue
> color #10 light blue
> save Pre0_wt_atRNA_range3.mrc models #9
> save Pre0_wt_ptRNA_range3.mrc models #10
> color #33 green
> save Pre0_wt_mRNA_range3.mrc models #33
> close #32
> show #!7 models
> show #!8 models
> view 1
> save C:\Users\anasc\Desktop\image3.png supersample 3
> color #10 deep sky blue
> color #9 blue
> color #9 cyan
> color #10 deeppink sly blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #10 deep sky blue
> save C:\Users\anasc\Desktop\image4.png supersample 3
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/EF-G_WT_states_20201010.cxs" includeMaps true
opened ChimeraX session
> view 1
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/images/WT/Pre0_wt_topview.png"
> width 3000 height 4000 supersample 4
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/images/WT/Pre0_wt_topview.png"
> width 3000 height 4000 supersample 4
> view name 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/images/WT/Pre0_wt_topview.png"
> width 3000 height 4000 supersample 4
> view name 2
> select #13
92140 atoms, 99978 bonds, 433 pseudobonds, 6872 residues, 2 models selected
> volume zone #12 nearAtoms sel range 4 newMap true
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!33 models
> hide #31 models
> select #21/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre1_wt_mRNA.pdb selectedOnly true
> cd
Current working directory is: C:\Users\anasc
> save Pre1_wt_mRNA.pdb selectedOnly true
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1/Pre1_wt_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
11 messages similar to the above omitted
Chain information for Pre1_wt_mRNA.pdb #18
---
Chain | Description
z | No description available
> select #14
52213 atoms, 56371 bonds, 176 pseudobonds, 4043 residues, 2 models selected
> volume zone #12 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #15
1643 atoms, 1834 bonds, 78 residues, 1 model selected
> volume zone #12 nearAtoms sel range 3 newMap true
> select #16
1637 atoms, 1821 bonds, 82 residues, 1 model selected
> volume zone #12 nearAtoms sel range 3 newMap true
> select #18
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #12 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> hide #!17 models
> show #!17 models
> save Pre1_wt_50S_range4.mrc models #17
> save Pre1_wt_30S_range4.mrc models #19
> save Pre1_wt_ptRNA_range3.mrc models #20
> save Pre1_wt_atRNA_range3.mrc models #27
> save Pre1_wt_mRNA_range3.mrc models #28
> color #20 deep sky blue
> color #28 green
> ui mousemode right select
> select clear
> ui mousemode right translate
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/images/WT/Pre1_wt_topview.png"
> width 3000 height 4000 supersample 4
> hide #!27 models
> hide #!28 models
> hide #!17 models
> hide #18 models
> show #18 models
> hide #!19 models
> hide #!20 models
> hide #18 models
> show #!21 models
> hide #!21 models
> show #!22 models
> select #23
92140 atoms, 99979 bonds, 433 pseudobonds, 6872 residues, 2 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #24
52213 atoms, 56371 bonds, 176 pseudobonds, 4043 residues, 2 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #25
1637 atoms, 1821 bonds, 82 residues, 1 model selected
> volume zone #22 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #26
1643 atoms, 1834 bonds, 78 residues, 1 model selected
> volume zone #22 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #21/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre2_wt_mRNA.pdb selectedOnly true
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2/Pre2_wt_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
12 messages similar to the above omitted
Chain information for Pre2_wt_mRNA.pdb #35
---
Chain | Description
z | No description available
> save Pre2_wt_50S_range4.mrc models #29
> save Pre2_wt_30S_range4.mrc models #30
> save Pre2_wt_atRNA_range3.mrc models #32
> save Pre2_wt_ptRNA_range3.mrc models #34
> select #35
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #22 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> save Pre2_wt_mRNA_range3.mrc models #36
> hide #!32 models
> hide #!30 models
> hide #!29 models
> show #!29 models
> show #!30 models
> show #!32 models
> hide #35 models
> view 2
> show #!33 models
> color #34 deep sky blue
> hide #!33 models
> color #36 green
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Figures/Pre2_wt_topview.png" width 3000 height 4000 supersample 4
> hide #!29 models
> hide #!30 models
> hide #!32 models
> hide #!34 models
> hide #!36 models
> show #!8 models
> show #!7 models
> show #!30 models
> show #!29 models
> hide #!29 models
> hide #!30 models
> hide #!7 models
> hide #!8 models
> ~select #35
Nothing selected
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/ChimeraX_sessions/Pre0-Pre1-Pre2_20201010.cxs" includeMaps true
opened ChimeraX session
> show #1 models
> hide #1 models
> show #1 models
> close #3-6,15-16,18,25-26,31,35#2,7-14,17,19-24,27-30,32-34,36
> hide #1 models
> show #1 models
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_sessions/test_session.cxs"
> includeMaps true
> hide #1 models
> close
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/G1 - P610L/latest maps/Pre0-g1.mrc"
Opened Pre0-g1.mrc, 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/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_wt_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_wt_50S.pdb
---
warnings | Ignored bad PDB record found on line 94314
END
Start residue of secondary structure not found: HELIX 116 116 THR b 19 TYR b
21 1 3
Start residue of secondary structure not found: HELIX 117 117 PRO b 24 PHE b
29 1 6
Start residue of secondary structure not found: HELIX 118 118 LEU b 42 SER b
61 1 20
Start residue of secondary structure not found: HELIX 119 119 ARG b 73 SER b
85 1 13
Start residue of secondary structure not found: HELIX 120 120 TRP b 103 GLN b
121 1 19
156 messages similar to the above omitted
Chain information for Pre0_wt_50S.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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_wt_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_wt_30S.pdb
---
warnings | Ignored bad PDB record found on line 53203
END
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
245 messages similar to the above omitted
Chain information for Pre0_wt_30S.pdb #3
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_P610L_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_P610L_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 2274
END
Ignored bad PDB record found on line 3203
END
Ignored bad PDB record found on line 3836
END
Ignored bad PDB record found on line 4804
END
Ignored bad PDB record found on line 5491
END
Start residue of secondary structure not found: HELIX 1 1 ILE x 6 ARG x 8 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS x 22 THR x 33 1
12
Start residue of secondary structure not found: HELIX 3 3 GLN x 54 GLU x 57 1
4
Start residue of secondary structure not found: HELIX 4 4 THR x 95 GLU x 97 1
3
Start residue of secondary structure not found: HELIX 5 5 VAL x 98 VAL x 104 1
7
91 messages similar to the above omitted
Chain information for Pre0_P610L_EF-G.pdb
---
Chain | Description
4.4/B | No description available
4.5/B | No description available
4.1/x | No description available
4.2/x | No description available
4.3/x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_P610L_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_P610L_atRNA.pdb
---
warning | Ignored bad PDB record found on line 1826
END
Chain information for Pre0_P610L_atRNA.pdb #5
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_wt_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_wt_ptRNA.pdb
---
warnings | Ignored bad PDB record found on line 2202
END
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
406 messages similar to the above omitted
Chain information for Pre0_wt_ptRNA.pdb #6
---
Chain | Description
v | No description available
> fitmap #2 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_wt_50S.pdb map 4.8 in map Pre0-g1.mrc using 343961 points
correlation = 0.8303, correlation about mean = 0.5635, overlap = 4.06e+05
steps = 80, shift = 3.19, angle = 4.02 degrees
Position of Pre0_wt_50S.pdb map 4.8 (#7) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99828079 0.02271815 0.05403097 -12.15676187
-0.02061535 0.99902018 -0.03916240 12.73410181
-0.05486773 0.03798120 0.99777100 1.09419447
Axis 0.54979489 0.77611041 -0.30883362
Axis point 25.69190880 0.00000000 254.93018115
Rotation angle (degrees) 4.02298792
Shift along axis 2.86141946
> fitmap #3 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_wt_30S.pdb map 4.8 in map Pre0-g1.mrc using 196177 points
correlation = 0.8101, correlation about mean = 0.4676, overlap = 2.079e+05
steps = 88, shift = 4.21, angle = 5.71 degrees
Position of Pre0_wt_30S.pdb map 4.8 (#8) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99785457 -0.04050916 -0.05143212 11.71260092
0.04425428 0.99628341 0.07389804 -14.72728835
0.04824742 -0.07601558 0.99593866 2.73079295
Axis -0.75339236 -0.50094052 0.42597951
Axis point 0.00000000 26.69031412 202.55565797
Rotation angle (degrees) 5.70994101
Shift along axis -0.28342671
> hide #3 models
> hide #2 models
> volume #1 step 1
> volume #1 level 3
> fitmap #4.1 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_P610L_EF-G.pdb map 4.8 in map Pre0-g1.mrc using 9265 points
correlation = 0.8014, correlation about mean = 0.4939, overlap = 5977
steps = 44, shift = 0.0308, angle = 0.177 degrees
Position of Pre0_P610L_EF-G.pdb map 4.8 (#9) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999758 -0.00050863 0.00213828 -0.19237464
0.00051325 0.99999753 -0.00216149 0.16905674
-0.00213718 0.00216258 0.99999538 0.22861215
Axis 0.70126016 0.69337550 0.16572448
Axis point 0.00000000 -104.01078837 71.85129152
Rotation angle (degrees) 0.17664752
Shift along axis 0.02020176
QWindowsWindow::setGeometry: Unable to set geometry 1920x1232+0+34 (frame:
1942x1288-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x616 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1288 maxtrack=0,0)
> fitmap #4.2 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_P610L_EF-G.pdb map 4.8 in map Pre0-g1.mrc using 3925 points
correlation = 0.7615, correlation about mean = 0.4631, overlap = 2016
steps = 44, shift = 0.084, angle = 0.346 degrees
Position of Pre0_P610L_EF-G.pdb map 4.8 (#10) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99998297 -0.00501297 0.00298941 -0.02101026
0.00500824 0.99998620 0.00158976 -1.14025865
-0.00299734 -0.00157476 0.99999427 0.75596341
Axis -0.26164618 0.49499296 0.82856699
Axis point 234.33851280 -1.46729002 0.00000000
Rotation angle (degrees) 0.34648762
Shift along axis 0.06744358
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #4.3 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_P610L_EF-G.pdb map 4.8 in map Pre0-g1.mrc using 2739 points
correlation = 0.7092, correlation about mean = 0.4668, overlap = 1242
steps = 44, shift = 0.0942, angle = 0.351 degrees
Position of Pre0_P610L_EF-G.pdb map 4.8 (#11) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99998395 -0.00471359 0.00314306 -0.02894490
0.00470628 0.99998621 0.00232941 -1.19492110
-0.00315400 -0.00231458 0.99999235 0.81251980
Axis -0.37923891 0.51423218 0.76924841
Axis point 256.23722000 -5.28013964 0.00000000
Rotation angle (degrees) 0.35081158
Shift along axis 0.02153972
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #4.4 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_P610L_EF-G.pdb map 4.8 in map Pre0-g1.mrc using 4092 points
correlation = 0.7231, correlation about mean = 0.1809, overlap = 2153
steps = 80, shift = 0.292, angle = 1.49 degrees
Position of Pre0_P610L_EF-G.pdb map 4.8 (#12) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99966221 -0.02483049 -0.00767574 3.89408458
0.02484030 0.99969073 0.00118533 -4.59588067
0.00764393 -0.00137560 0.99996984 -1.27974719
Axis -0.04920839 -0.29436759 0.95442457
Axis point 187.64934818 154.15469853 0.00000000
Rotation angle (degrees) 1.49108087
Shift along axis -0.06016547
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #4.5 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_P610L_EF-G.pdb map 4.8 in map Pre0-g1.mrc using 2949 points
correlation = 0.6358, correlation about mean = 0.2784, overlap = 1202
steps = 60, shift = 0.139, angle = 0.359 degrees
Position of Pre0_P610L_EF-G.pdb map 4.8 (#13) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999071 0.00404377 0.00149370 -0.81081339
-0.00403693 0.99998147 -0.00455761 1.57120590
-0.00151210 0.00455154 0.99998850 -0.19445323
Axis 0.72627433 0.23965361 -0.64427614
Axis point 0.00000000 55.92621308 349.09330182
Rotation angle (degrees) 0.35931248
Shift along axis -0.08704620
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #5 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_P610L_atRNA.pdb map 4.8 in map Pre0-g1.mrc using 6166 points
correlation = 0.8033, correlation about mean = 0.3969, overlap = 5681
steps = 40, shift = 0.0513, angle = 0.112 degrees
Position of Pre0_P610L_atRNA.pdb map 4.8 (#14) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999845 0.00173596 0.00028429 -0.34056442
-0.00173571 0.99999813 -0.00084940 0.45505035
-0.00028576 0.00084890 0.99999960 -0.05710860
Axis 0.43472299 0.14591822 -0.88866405
Axis point 264.56383603 188.68023141 0.00000000
Rotation angle (degrees) 0.11191638
Shift along axis -0.03090069
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #6 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_wt_ptRNA.pdb map 4.8 in map Pre0-g1.mrc using 6191 points
correlation = 0.4503, correlation about mean = 0.05385, overlap = 3125
steps = 152, shift = 23.3, angle = 16.7 degrees
Position of Pre0_wt_ptRNA.pdb map 4.8 (#15) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.96479956 -0.17816160 0.19344317 -28.76848753
0.15372410 0.97887013 0.13484125 -55.55868389
-0.21337928 -0.10035790 0.97180120 60.02014036
Axis -0.40882797 0.70714710 0.57689052
Axis point 238.68223158 0.00000000 177.14889901
Rotation angle (degrees) 16.71734751
Shift along axis 7.09824965
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #6
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> fitmap #6 inMap #1 resolution 4.8 metric correlation
Fit map Pre0_wt_ptRNA.pdb map 4.8 in map Pre0-g1.mrc using 6191 points
correlation = 0.7124, correlation about mean = 0.2724, overlap = 5179
steps = 124, shift = 11.2, angle = 22.3 degrees
Position of Pre0_wt_ptRNA.pdb map 4.8 (#15) relative to Pre0-g1.mrc (#1)
coordinates:
Matrix rotation and translation
0.67467302 -0.61676653 -0.40548164 214.72580900
0.48810688 0.78488543 -0.38171525 43.19914926
0.55368582 0.05961460 0.83058901 -58.03082855
Axis 0.28878295 -0.62762855 0.72297083
Axis point 61.22857943 319.15620232 0.00000000
Rotation angle (degrees) 49.82879589
Shift along axis -7.05846199
> ui mousemode right translate
> close #9-15
> save Pre0_p610l_50S.pdb models #2
> cd
Current working directory is: C:\Users\anasc
> save Pre0_p610l_50S.pdb models #2
> save Pre0_p610l_30S.pdb models #3
> save Pre0_p610l_EF-G.pdb models #4
> save Pre0_p610l_atRNA.pdb models #5
> save Pre0_p610l_ptRNA.pdb models #6
> close #7-8
> select #3/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> show #3 models
> hide #!1 models
> hide #3 models
> show #3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> select up
52207 atoms, 56371 bonds, 4037 residues, 1 model selected
> select #3/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre0_p610l_mRNA.pdb selectedOnly true
> hide #3 models
> close #2-3,5-6#4
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb
---
warning | Ignored bad PDB record found on line 94153
END
Chain information for Pre0_p610l_50S.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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb
---
warning | Ignored bad PDB record found on line 52953
END
Chain information for Pre0_p610l_30S.pdb #3
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb
---
warning | Ignored bad PDB record found on line 1826
END
Chain information for Pre0_p610l_atRNA.pdb #4
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 2274
END
Ignored bad PDB record found on line 3203
END
Ignored bad PDB record found on line 3836
END
Ignored bad PDB record found on line 4804
END
Ignored bad PDB record found on line 5491
END
Start residue of secondary structure not found: HELIX 1 1 ILE x 6 ARG x 8 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS x 22 THR x 33 1
12
Start residue of secondary structure not found: HELIX 3 3 GLN x 54 GLU x 57 1
4
Start residue of secondary structure not found: HELIX 4 4 THR x 95 GLU x 97 1
3
Start residue of secondary structure not found: HELIX 5 5 VAL x 98 VAL x 104 1
7
91 messages similar to the above omitted
Chain information for Pre0_p610l_EF-G.pdb
---
Chain | Description
5.4/B | No description available
5.5/B | No description available
5.1/x | No description available
5.2/x | No description available
5.3/x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 253
END
Ignored bad PDB record found on line 506
END
Ignored bad PDB record found on line 509
END
Ignored bad PDB record found on line 512
END
Ignored bad PDB record found on line 515
END
4 messages similar to the above omitted
Chain information for Pre0_p610l_mRNA.pdb #6
---
Chain | Description
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb
---
warning | Ignored bad PDB record found on line 1791
END
Chain information for Pre0_p610l_ptRNA.pdb #7
---
Chain | Description
v | No description available
> select #2
92129 atoms, 99979 bonds, 6860 residues, 1 model selected
> show #!1 models
> hide #!1 models
> volume zone #1 nearAtoms sel range 4 newMap true
> hide #2 models
> show #!1 models
> hide #!1 models
> show #2 models
> select #3
52207 atoms, 56371 bonds, 4037 residues, 1 model selected
> volume zone #1 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1064+0+34 (frame:
1942x1120-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x532 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1120 maxtrack=0,0)
> hide #3 models
> hide #2 models
> select #5
5404 atoms, 5503 bonds, 697 residues, 6 models selected
> volume zone #1 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1232+0+34 (frame:
1942x1288-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x616 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1288 maxtrack=0,0)
> select #4
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> volume zone #1 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #6
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #1 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> select #7
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> volume zone #1 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> view 2
> close #2-4,6-7#5
> save Pre0_p610l_50S.mrc models #8
> save Pre0_p610l_30S.mrc models #9
> save Pre0_p610l_EF-G.mrc models #10
> save Pre0_p610l_atRNA.mrc models #11
> save Pre0_p610l_mRNA.mrc models #12
> save Pre0_p610l_ptRNA.mrc models #13
> color #10 red
> color #12 green
> color #13 deep sky blue
> select 1-13
Expected an objects specifier or a keyword
> select #1-13
14 models selected
> volume sel & #!8-13 step 1
> volume sel level 3
> ui mousemode right select
> select clear
> ui mousemode right translate
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Figures/Pre0_P610L_topview.png"
> width 3000 height 4000 supersample 4
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_sessions/Pre0_p610l.cxs"
> includeMaps true
> rename #8 id #2
> rename #9 id #3
> rename #10 id #4
> rename #11 id #5
> rename #12 id #6
> rename #13 id #7
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> open C:/Users/anasc/Pre1-1-g1.mrc
Opened Pre1-1-g1.mrc, grid size 288,288,288, pixel 1.16, shown at level 4.03,
step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> close #8
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/P610L_Pre_3d512_33A_sharp.mrc"
Opened P610L_Pre_3d512_33A_sharp.mrc, grid size 512,512,512, pixel 0.652,
shown at level 4.36, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb
---
warning | Ignored bad PDB record found on line 52953
END
Chain information for Pre0_p610l_30S.pdb #9
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb
---
warning | Ignored bad PDB record found on line 94153
END
Chain information for Pre0_p610l_50S.pdb #10
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb
---
warning | Ignored bad PDB record found on line 1826
END
Chain information for Pre0_p610l_atRNA.pdb #11
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 2274
END
Ignored bad PDB record found on line 3203
END
Ignored bad PDB record found on line 3836
END
Ignored bad PDB record found on line 4804
END
Ignored bad PDB record found on line 5491
END
Start residue of secondary structure not found: HELIX 1 1 ILE x 6 ARG x 8 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS x 22 THR x 33 1
12
Start residue of secondary structure not found: HELIX 3 3 GLN x 54 GLU x 57 1
4
Start residue of secondary structure not found: HELIX 4 4 THR x 95 GLU x 97 1
3
Start residue of secondary structure not found: HELIX 5 5 VAL x 98 VAL x 104 1
7
91 messages similar to the above omitted
Chain information for Pre0_p610l_EF-G.pdb
---
Chain | Description
12.4/B | No description available
12.5/B | No description available
12.1/x | No description available
12.2/x | No description available
12.3/x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb
---
warning | Ignored bad PDB record found on line 1791
END
Chain information for Pre0_p610l_ptRNA.pdb #13
---
Chain | Description
v | No description available
> fitmap #9 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_30S.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
439515 points
correlation = 0.765, correlation about mean = 0.4222, overlap = 7.824e+05
steps = 52, shift = 0.339, angle = 0.432 degrees
Position of Pre0_p610l_30S.pdb map 3.3 (#14) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99997209 -0.00060438 0.00744613 -0.90487275
0.00061177 0.99999932 -0.00099125 0.18413769
-0.00744553 0.00099577 0.99997179 0.81939932
Axis 0.13182818 0.98798341 0.08068528
Axis point 108.18659841 0.00000000 124.20735767
Rotation angle (degrees) 0.43180768
Shift along axis 0.12875072
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #10 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_50S.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
773912 points
correlation = 0.8174, correlation about mean = 0.5675, overlap = 1.681e+06
steps = 68, shift = 0.0864, angle = 0.434 degrees
Position of Pre0_p610l_50S.pdb map 3.3 (#15) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99998574 -0.00041083 0.00532415 -0.85641673
0.00043945 0.99998545 -0.00537704 0.79848196
-0.00532186 0.00537931 0.99997137 -0.09873278
Axis 0.70962375 0.70234428 0.05609504
Axis point -0.00000000 18.63365538 155.30056235
Rotation angle (degrees) 0.43424369
Shift along axis -0.05246283
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #11 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_atRNA.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc
using 13374 points
correlation = 0.7732, correlation about mean = 0.3359, overlap = 2.177e+04
steps = 52, shift = 0.447, angle = 1.31 degrees
Position of Pre0_p610l_atRNA.pdb map 3.3 (#16) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99983001 0.00457473 0.01786125 -3.74477127
-0.00433083 0.99989718 -0.01366993 3.42580271
-0.01792195 0.01359025 0.99974702 1.05578705
Axis 0.59446057 0.78032166 -0.19420283
Axis point 58.45234473 0.00000000 218.27190388
Rotation angle (degrees) 1.31382138
Shift along axis 0.24207236
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #13 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_ptRNA.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc
using 13490 points
correlation = 0.638, correlation about mean = 0.1594, overlap = 1.703e+04
steps = 68, shift = 0.76, angle = 2.13 degrees
Position of Pre0_p610l_ptRNA.pdb map 3.3 (#17) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99932831 0.00072738 0.03663871 -8.34315770
-0.00051030 0.99998226 -0.00593411 1.97693441
-0.03664238 0.00591142 0.99931096 4.62860325
Axis 0.15955160 0.98704882 -0.01667072
Axis point 122.19670596 0.00000000 232.31911022
Rotation angle (degrees) 2.12738317
Shift along axis 0.54300446
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #12.1 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
19961 points
correlation = 0.7775, correlation about mean = 0.4523, overlap = 2.435e+04
steps = 64, shift = 0.388, angle = 0.557 degrees
Position of Pre0_p610l_EF-G.pdb map 3.3 (#18) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99998578 -0.00446280 0.00291799 0.14000736
0.00443894 0.99995707 0.00813324 -1.82568423
-0.00295416 -0.00812017 0.99996267 1.11692110
Axis -0.83609983 0.30207205 0.45791871
Axis point 0.00000000 145.39888307 219.40495551
Rotation angle (degrees) 0.55691124
Shift along axis -0.15708923
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #12.2 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
8298 points
correlation = 0.7565, correlation about mean = 0.4127, overlap = 8533
steps = 52, shift = 0.549, angle = 0.831 degrees
Position of Pre0_p610l_EF-G.pdb map 3.3 (#19) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99991012 -0.00499234 0.01244322 -0.71272026
0.00492331 0.99997236 0.00557187 -1.65934375
-0.01247069 -0.00551010 0.99990706 2.65081723
Axis -0.38194778 0.85867512 0.34174981
Axis point 218.82932318 0.00000000 66.43100773
Rotation angle (degrees) 0.83122915
Shift along axis -0.24669900
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #12.3 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
5640 points
correlation = 0.728, correlation about mean = 0.4359, overlap = 5559
steps = 68, shift = 0.739, angle = 2.03 degrees
Position of Pre0_p610l_EF-G.pdb map 3.3 (#20) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99976471 -0.01366147 0.01684929 -0.39943851
0.01318436 0.99951790 0.02810950 -6.45021520
-0.01722519 -0.02788074 0.99946283 6.11734362
Axis -0.79050437 0.48108439 0.37902591
Axis point 0.00000000 221.44332889 225.24362902
Rotation angle (degrees) 2.02951125
Shift along axis -0.46870821
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #12.4 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
8706 points
correlation = 0.6489, correlation about mean = 0.1334, overlap = 5645
steps = 96, shift = 3.62, angle = 8.66 degrees
Position of Pre0_p610l_EF-G.pdb map 3.3 (#21) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99528221 0.01156952 -0.09633003 15.78700987
-0.00035441 0.99329165 0.11563555 -18.48867608
0.09702166 -0.11505587 0.98860960 -4.19869000
Axis -0.76580587 -0.64185246 -0.03958282
Axis point 0.00000000 -52.07279230 157.18067194
Rotation angle (degrees) 8.66286037
Shift along axis -0.05658662
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> fitmap #12.5 inMap #8 resolution 3.3 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.3 in map P610L_Pre_3d512_33A_sharp.mrc using
6171 points
correlation = 0.7, correlation about mean = 0.3233, overlap = 5849
steps = 72, shift = 1.58, angle = 6.57 degrees
Position of Pre0_p610l_EF-G.pdb map 3.3 (#22) relative to
P610L_Pre_3d512_33A_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99450865 0.10280573 -0.01958393 -5.88946490
-0.10179060 0.99368436 0.04722352 15.29108129
0.02431509 -0.04497074 0.99869235 -0.95719561
Axis -0.40318918 -0.19198166 -0.89475222
Axis point 146.80904933 63.97052893 0.00000000
Rotation angle (degrees) 6.56505579
Shift along axis 0.29541431
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> close #14-22
> save Pre1_33A_p610l_30S.pdb models #9
> save Pre1_33A_p610l_50S.pdb models #10
> save Pre1_33A_p610l_atRNA.pdb models #11
> save Pre1_33A_p610l_ptRNA.pdb models #13
> save Pre1_33A_p610l_EF-G.pdb models #12
> close #9-11,13#12
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_50S.pdb
---
warning | Ignored bad PDB record found on line 94153
END
Chain information for Pre1_33A_p610l_50S.pdb #9
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_30S.pdb
---
warning | Ignored bad PDB record found on line 52953
END
Chain information for Pre1_33A_p610l_30S.pdb #10
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_atRNA.pdb
---
warning | Ignored bad PDB record found on line 1826
END
Chain information for Pre1_33A_p610l_atRNA.pdb #11
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 2274
END
Ignored bad PDB record found on line 3203
END
Ignored bad PDB record found on line 3836
END
Ignored bad PDB record found on line 4804
END
Ignored bad PDB record found on line 5491
END
Start residue of secondary structure not found: HELIX 1 1 ILE x 6 ARG x 8 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS x 22 THR x 33 1
12
Start residue of secondary structure not found: HELIX 3 3 GLN x 54 GLU x 57 1
4
Start residue of secondary structure not found: HELIX 4 4 THR x 95 GLU x 97 1
3
Start residue of secondary structure not found: HELIX 5 5 VAL x 98 VAL x 104 1
7
91 messages similar to the above omitted
Chain information for Pre1_33A_p610l_EF-G.pdb
---
Chain | Description
12.4/B | No description available
12.5/B | No description available
12.1/x | No description available
12.2/x | No description available
12.3/x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre1/Pre1_33A_p610l_ptRNA.pdb
---
warning | Ignored bad PDB record found on line 1791
END
Chain information for Pre1_33A_p610l_ptRNA.pdb #13
---
Chain | Description
v | No description available
> select #10/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre1_33A_p610l_mRNA.pdb selectedOnly true
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre1_33A_p610l_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre1_33A_p610l_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 253
END
Ignored bad PDB record found on line 506
END
Ignored bad PDB record found on line 509
END
Ignored bad PDB record found on line 512
END
Ignored bad PDB record found on line 515
END
4 messages similar to the above omitted
Chain information for Pre1_33A_p610l_mRNA.pdb #14
---
Chain | Description
z | No description available
> select #9
92129 atoms, 99979 bonds, 6860 residues, 1 model selected
> volume zone #8 nearAtoms sel range 4 newMap true
> select #10
52207 atoms, 56371 bonds, 4037 residues, 1 model selected
> volume zone #8 nearAtoms sel range 4 newMap true
> select #12
5404 atoms, 5503 bonds, 697 residues, 6 models selected
> volume zone #8 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> select #11
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> volume zone #8 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> select #13
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> volume zone #8 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> select #14
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #8 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> hide #9 models
> hide #10 models
> hide #11 models
> hide #!12 models
> hide #13 models
> hide #14 models
> save Pre1_33A_p610l_50S_range4.mrc models #15
> save Pre1_33A_p610l_350S_range4.mrc models #16
> save Pre1_33A_p610l_EF-G_range4.mrc models #17
> save Pre1_33A_p610l_atRNA_range3.mrc models #18
> save Pre1_33A_p610l_ptRNA_range3.mrc models #19
> save Pre1_33A_p610l_mRNA_range3.mrc models #20
> close #9-11,13-14#12
> color #17 red
> color #19 deep sky blue
> color #20 green
> select #8-20
14 models selected
> volume sel & #!15-20 step 1
> volume sel level 3
> ui mousemode right select
> select clear
> ui mousemode right translate
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!16 models
> show #!16 models
> hide #!3 models
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Figures/Pre1_33A_P610L_topview.png"
> width 3000 height 4000 supersample 4
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> rename #15 id #9
> rename #16 id #10
> rename #17 id #11
> rename #18 id #12
> rename #19 id #13
> rename #20 id #14
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_sessions/Pre0-Pre1_p610l.cxs"
> includeMaps true
opened ChimeraX session
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G1/P610L_Pre1-1-g1.mrc"
Opened P610L_Pre1-1-g1.mrc, grid size 288,288,288, pixel 1.16, shown at level
4.03, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_volumes/Pre1-1_p610l_30S_range4.mrc"
Opened Pre1-1_p610l_30S_range4.mrc, grid size 288,288,288, pixel 1.16, shown
at level 2.02, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_volumes/Pre1-1_p610l_50S_range4.mrc"
Opened Pre1-1_p610l_50S_range4.mrc, grid size 288,288,288, pixel 1.16, shown
at level 3.18, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_volumes/Pre1-1_p610l_atRNA_range3.mrc"
Opened Pre1-1_p610l_atRNA_range3.mrc, grid size 288,288,288, pixel 1.16, shown
at level 8.46e-05, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_volumes/Pre1-1_p610l_EF-
> G_range4.mrc"
Opened Pre1-1_p610l_EF-G_range4.mrc, grid size 288,288,288, pixel 1.16, shown
at level 0.00108, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_volumes/Pre1-1_p610l_mRNA_range3.mrc"
Opened Pre1-1_p610l_mRNA_range3.mrc, grid size 288,288,288, pixel 1.16, shown
at level 0.00106, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_volumes/Pre1-1_p610l_ptRNA_range3.mrc"
Opened Pre1-1_p610l_ptRNA_range3.mrc, grid size 288,288,288, pixel 1.16, shown
at level 0.000577, step 2, values float32
> select #15-21
14 models selected
> volume sel step 1
> volume sel level 3
> hide #!16 models
> hide #!15 models
> show #!16 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> color #19 red
> color #20 green
> color #21 deep sky blue
> view 2
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G1/P610L_Pre1-2-g1.mrc"
Opened P610L_Pre1-2-g1.mrc, grid size 288,288,288, pixel 1.16, shown at level
4.36, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb
---
warning | Ignored bad PDB record found on line 52953
END
Chain information for Pre0_p610l_30S.pdb #23
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb
---
warning | Ignored bad PDB record found on line 94153
END
Chain information for Pre0_p610l_50S.pdb #24
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb
---
warning | Ignored bad PDB record found on line 1826
END
Chain information for Pre0_p610l_atRNA.pdb #25
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 2274
END
Ignored bad PDB record found on line 3203
END
Ignored bad PDB record found on line 3836
END
Ignored bad PDB record found on line 4804
END
Ignored bad PDB record found on line 5491
END
Start residue of secondary structure not found: HELIX 1 1 ILE x 6 ARG x 8 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS x 22 THR x 33 1
12
Start residue of secondary structure not found: HELIX 3 3 GLN x 54 GLU x 57 1
4
Start residue of secondary structure not found: HELIX 4 4 THR x 95 GLU x 97 1
3
Start residue of secondary structure not found: HELIX 5 5 VAL x 98 VAL x 104 1
7
91 messages similar to the above omitted
Chain information for Pre0_p610l_EF-G.pdb
---
Chain | Description
26.4/B | No description available
26.5/B | No description available
26.1/x | No description available
26.2/x | No description available
26.3/x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb
---
warning | Ignored bad PDB record found on line 1791
END
Chain information for Pre0_p610l_ptRNA.pdb #27
---
Chain | Description
v | No description available
> fitmap #23 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_30S.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 313335
points
correlation = 0.8041, correlation about mean = 0.4502, overlap = 4.345e+05
steps = 64, shift = 0.267, angle = 0.276 degrees
Position of Pre0_p610l_30S.pdb map 3.9 (#28) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99998859 -0.00058548 0.00474151 -0.52071267
0.00058839 0.99999964 -0.00061346 0.12616928
-0.00474115 0.00061624 0.99998857 0.49080399
Axis 0.12764442 0.98430683 0.12184816
Axis point 100.22670483 0.00000000 113.22520207
Rotation angle (degrees) 0.27599024
Shift along axis 0.11752678
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #24 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_50S.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 550766
points
correlation = 0.8439, correlation about mean = 0.5855, overlap = 8.744e+05
steps = 52, shift = 0.102, angle = 0.377 degrees
Position of Pre0_p610l_50S.pdb map 3.9 (#29) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99999092 -0.00028476 0.00425205 -0.67239908
0.00030605 0.99998741 -0.00500806 0.79354594
-0.00425057 0.00500931 0.99997842 -0.27691683
Axis 0.76162574 0.64645842 0.04491919
Axis point 0.00000000 55.86519085 159.80576695
Rotation angle (degrees) 0.37679736
Shift along axis -0.01156088
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #25 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_atRNA.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 9614
points
correlation = 0.8069, correlation about mean = 0.3627, overlap = 1.271e+04
steps = 76, shift = 0.341, angle = 0.655 degrees
Position of Pre0_p610l_atRNA.pdb map 3.9 (#30) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99996224 0.00120848 0.00860587 -1.58537111
-0.00114460 0.99997179 -0.00742372 1.67365628
-0.00861460 0.00741359 0.99993541 0.28721166
Axis 0.64926990 0.75355558 -0.10296885
Axis point 34.26122687 0.00000000 199.63138958
Rotation angle (degrees) 0.65468440
Shift along axis 0.20228544
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #26.1 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 14494
points
correlation = 0.8228, correlation about mean = 0.5158, overlap = 1.362e+04
steps = 68, shift = 0.382, angle = 0.626 degrees
Position of Pre0_p610l_EF-G.pdb map 3.9 (#31) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99999546 -0.00300943 0.00014775 0.34331206
0.00300772 0.99994036 0.01049911 -1.83754623
-0.00017933 -0.01049862 0.99994487 0.75474757
Axis -0.96120067 0.01497259 0.27544346
Axis point 0.00000000 74.89532087 175.23124885
Rotation angle (degrees) 0.62583478
Shift along axis -0.14961433
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #26.2 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 6062
points
correlation = 0.8065, correlation about mean = 0.4788, overlap = 4875
steps = 64, shift = 0.575, angle = 1.02 degrees
Position of Pre0_p610l_EF-G.pdb map 3.9 (#32) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99986002 -0.00074671 0.01671498 -1.65783473
0.00085061 0.99998036 -0.00620977 0.68654863
-0.01671002 0.00622312 0.99984101 2.37309787
Axis 0.34827796 0.93632278 0.04474491
Axis point 140.56798560 0.00000000 103.93585324
Rotation angle (degrees) 1.02273138
Shift along axis 0.17162789
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #26.3 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 4160
points
correlation = 0.7743, correlation about mean = 0.5036, overlap = 3282
steps = 52, shift = 0.662, angle = 1.81 degrees
Position of Pre0_p610l_EF-G.pdb map 3.9 (#33) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99988992 -0.01038970 0.01059264 0.04138095
0.01009078 0.99955999 0.02789278 -5.79255732
-0.01087777 -0.02778282 0.99955480 4.86826007
Axis -0.88249536 0.34032025 0.32462913
Axis point 0.00000000 176.93125943 205.24788590
Rotation angle (degrees) 1.80766193
Shift along axis -0.42746404
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #26.4 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 6371
points
correlation = 0.6691, correlation about mean = 0.1405, overlap = 3467
steps = 76, shift = 4.44, angle = 6.3 degrees
Position of Pre0_p610l_EF-G.pdb map 3.9 (#34) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99756990 0.04710155 -0.05133946 2.71936150
-0.04256937 0.99538048 0.08605548 -4.61097280
0.05515564 -0.08366086 0.99496669 -0.74650397
Axis -0.77315131 -0.48514375 -0.40850042
Axis point 0.00000000 -9.82006999 50.57679899
Rotation angle (degrees) 6.30126324
Shift along axis 0.43945391
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #26.5 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 4538
points
correlation = 0.7379, correlation about mean = 0.3784, overlap = 3515
steps = 76, shift = 1.58, angle = 5.96 degrees
Position of Pre0_p610l_EF-G.pdb map 3.9 (#35) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99573535 0.08822725 -0.02696409 -3.59247135
-0.08683429 0.99501321 0.04907660 11.83232792
0.03115952 -0.04652590 0.99843098 -2.15373493
Axis -0.46015557 -0.27976158 -0.84260923
Axis point 134.10766145 46.37867291 -0.00000000
Rotation angle (degrees) 5.96267832
Shift along axis 0.15762189
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #27 inMap #22 resolution 3.9 metric correlation
Fit map Pre0_p610l_ptRNA.pdb map 3.9 in map P610L_Pre1-2-g1.mrc using 9642
points
correlation = 0.6967, correlation about mean = 0.2101, overlap = 1.055e+04
steps = 52, shift = 0.591, angle = 1.54 degrees
Position of Pre0_p610l_ptRNA.pdb map 3.9 (#36) relative to P610L_Pre1-2-g1.mrc
(#22) coordinates:
Matrix rotation and translation
0.99966244 0.00155718 0.02593403 -6.09519199
-0.00174241 0.99997313 0.00712130 -0.77978188
-0.02592225 -0.00716408 0.99963829 5.36772085
Axis -0.26508852 0.96227805 -0.06122935
Axis point 205.09767805 0.00000000 232.20999128
Rotation angle (degrees) 1.54399527
Shift along axis 0.53673640
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> close #28-36
> select #23/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre1-2_p610l_mRNA.pdb selectedOnly true
> save Pre1-2_p610l_30S.pdb models #23
> save Pre1-2_p610l_50S.pdb models #24
> save Pre1-2_p610l_atRNA.pdb models #25
> save Pre1-2_p610l_EF-G.pdb models #26
> save Pre1-2_p610l_ptRNA.pdb models #27
> cd
Current working directory is: C:\Users\anasc
> save Pre1-2_p610l_ptRNA.pdb models #27
> save Pre1-2_p610l_EF-G.pdb models #26
> save Pre1-2_p610l_atRNA.pdb models #25
> save Pre1-2_p610l_50S.pdb models #24
> save Pre1-2_p610l_30S.pdb models #23
> select #23/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre1-2_p610l_mRNA.pdb selectedOnly true
> select #23
52207 atoms, 56371 bonds, 4037 residues, 1 model selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> close #28
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Pre1-2/Pre1-2_p610l_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre1-2/Pre1-2_p610l_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
4 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 THR b 19 TYR b 21 1
3
Start residue of secondary structure not found: HELIX 2 2 PRO b 24 PHE b 29 1
6
Start residue of secondary structure not found: HELIX 3 3 LEU b 42 SER b 61 1
20
Start residue of secondary structure not found: HELIX 4 4 ARG b 73 SER b 85 1
13
Start residue of secondary structure not found: HELIX 5 5 TRP b 103 GLN b 121
1 19
156 messages similar to the above omitted
Chain information for Pre1-2_p610l_mRNA.pdb #28
---
Chain | Description
z | No description available
> select #23
52207 atoms, 56371 bonds, 4037 residues, 1 model selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #24
92129 atoms, 99979 bonds, 6860 residues, 1 model selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #26
5404 atoms, 5503 bonds, 697 residues, 6 models selected
> volume zone #22 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #25
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> volume zone #22 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #27
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> volume zone #22 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #28
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #22 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> close #23-25,27-28#26
> hide #!3 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> select #22-34
14 models selected
> volume sel & #!29-34 step 1
> volume sel level 0.02
> volume sel level 3
> ui mousemode right select
> select clear
> ui mousemode right translate
> view 2
> save Pre1-2_p610l_30S.mrc models #29
> save Pre1-2_p610l_50S.mrc models #30
> save Pre1-2_p610l_EF-G.mrc models #31
> save Pre1-2_p610l_EF-G_range3.mrc models #31
> save Pre1-2_p610l_30S_range4.mrc models #29
> save Pre1-2_p610l_EF-G_range4.mrc models #31
> save Pre1-2_p610l_50S_range4.mrc models #30
> save Pre1-2_p610l_atRNA_range3.mrc models #31
> hide #!31 models
> show #!31 models
> save Pre1-2_p610l_EF-G_range4.mrc models #31
> save Pre1-2_p610l_atRNA_range3.mrc models #32
> save Pre1-2_p610l_ptRNA_range3.mrc models #33
> save Pre1-2_p610l_mRNA_range3.mrc models #34
> color #31 red
> color #33 deep sky blue
> color #34 green
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Figures/Pre1-2_P610L_topview.png"
> width 3000 height 4000 supersample 4
> rename #29 id #23
> rename #30 id #24
> rename #31 id #25
> rename #32 id #26
> rename #33 id #27
> rename #34 id #28
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G1/P610L_Pre2-g1.mrc"
Opened P610L_Pre2-g1.mrc, grid size 288,288,288, pixel 1.16, shown at level
4.27, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_30S.pdb
---
warning | Ignored bad PDB record found on line 52953
END
Chain information for Pre0_p610l_30S.pdb #30
---
Chain | Description
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
y | No description available
z | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_50S.pdb
---
warning | Ignored bad PDB record found on line 94153
END
Chain information for Pre0_p610l_50S.pdb #31
---
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
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_atRNA.pdb
---
warning | Ignored bad PDB record found on line 1826
END
Chain information for Pre0_p610l_atRNA.pdb #32
---
Chain | Description
w | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 2274
END
Ignored bad PDB record found on line 3203
END
Ignored bad PDB record found on line 3836
END
Ignored bad PDB record found on line 4804
END
Ignored bad PDB record found on line 5491
END
Start residue of secondary structure not found: HELIX 1 1 ILE x 6 ARG x 8 1 3
Start residue of secondary structure not found: HELIX 2 2 LYS x 22 THR x 33 1
12
Start residue of secondary structure not found: HELIX 3 3 GLN x 54 GLU x 57 1
4
Start residue of secondary structure not found: HELIX 4 4 THR x 95 GLU x 97 1
3
Start residue of secondary structure not found: HELIX 5 5 VAL x 98 VAL x 104 1
7
91 messages similar to the above omitted
Chain information for Pre0_p610l_EF-G.pdb
---
Chain | Description
33.4/B | No description available
33.5/B | No description available
33.1/x | No description available
33.2/x | No description available
33.3/x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/ChimeraX_pdbs/Pre0_p610l_ptRNA.pdb
---
warning | Ignored bad PDB record found on line 1791
END
Chain information for Pre0_p610l_ptRNA.pdb #34
---
Chain | Description
v | No description available
> hide #!29 models
> fitmap #30 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_30S.pdb map 7.9 in map P610L_Pre2-g1.mrc using 57779 points
correlation = 0.8626, correlation about mean = 0.6169, overlap = 4.768e+04
steps = 48, shift = 0.429, angle = 0.72 degrees
Position of Pre0_p610l_30S.pdb map 7.9 (#35) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99992705 -0.00925145 -0.00776558 2.05241025
0.00927847 0.99995100 0.00345035 -1.63692118
0.00773328 -0.00352215 0.99996389 -0.48565391
Axis -0.27730952 -0.61642008 0.73697064
Axis point 172.15348168 222.94689886 0.00000000
Rotation angle (degrees) 0.72032298
Shift along axis 0.08196551
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #31 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_50S.pdb map 7.9 in map P610L_Pre2-g1.mrc using 100806
points
correlation = 0.8655, correlation about mean = 0.6563, overlap = 8.687e+04
steps = 48, shift = 0.255, angle = 0.46 degrees
Position of Pre0_p610l_50S.pdb map 7.9 (#36) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99998862 -0.00419063 0.00227970 0.24588928
0.00420528 0.99997029 -0.00645970 0.38090964
-0.00225256 0.00646921 0.99997654 -0.76997673
Axis 0.80462371 0.28206304 0.52251423
Axis point -0.00000000 111.41160048 62.69175004
Rotation angle (degrees) 0.46032713
Shift along axis -0.09703492
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #32 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_atRNA.pdb map 7.9 in map P610L_Pre2-g1.mrc using 2083
points
correlation = 0.855, correlation about mean = 0.6119, overlap = 1562
steps = 112, shift = 8.5, angle = 32.8 degrees
Position of Pre0_p610l_atRNA.pdb map 7.9 (#37) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.86472505 -0.16219654 -0.47533448 134.37267914
0.26548084 0.95100614 0.15845269 -67.06049088
0.42634553 -0.26321021 0.86541890 -9.10701268
Axis -0.38920685 -0.83227630 0.39475839
Axis point 101.39111541 0.00000000 253.76968851
Rotation angle (degrees) 32.79910732
Shift along axis -0.08097889
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #33.1 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 7.9 in map P610L_Pre2-g1.mrc using 2748 points
correlation = 0.8243, correlation about mean = 0.5822, overlap = 1257
steps = 80, shift = 0.86, angle = 1.55 degrees
Position of Pre0_p610l_EF-G.pdb map 7.9 (#38) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99970773 0.01365389 -0.01995074 1.92779859
-0.01341296 0.99983610 0.01216021 1.20797009
0.02011351 -0.01188906 0.99972701 -2.71858736
Axis -0.44534731 -0.74191450 -0.50122715
Axis point 146.09752285 0.00000000 85.73457195
Rotation angle (degrees) 1.54720750
Shift along axis -0.39212065
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #33.2 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 7.9 in map P610L_Pre2-g1.mrc using 1251 points
correlation = 0.7951, correlation about mean = 0.5329, overlap = 439.4
steps = 52, shift = 0.874, angle = 0.388 degrees
Position of Pre0_p610l_EF-G.pdb map 7.9 (#39) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99997776 0.00304096 -0.00593584 1.29508372
-0.00304780 0.99999470 -0.00114299 0.71335803
0.00593233 0.00116106 0.99998173 -0.82569163
Axis 0.17021078 -0.87675741 -0.44980523
Axis point 142.40628480 0.00000000 218.61046956
Rotation angle (degrees) 0.38779321
Shift along axis -0.03360431
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #33.3 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 7.9 in map P610L_Pre2-g1.mrc using 917 points
correlation = 0.6842, correlation about mean = 0.5952, overlap = 256.9
steps = 68, shift = 1.82, angle = 7.19 degrees
Position of Pre0_p610l_EF-G.pdb map 7.9 (#40) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99398955 0.01609086 -0.10828605 17.59266208
-0.00946387 0.99806610 0.06143691 -7.30300586
0.10906521 -0.06004284 0.99221955 -12.31752736
Axis -0.48532944 -0.86835015 -0.10209488
Axis point 124.61253209 0.00000000 151.33901935
Rotation angle (degrees) 7.18952505
Shift along axis -0.93911406
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #33.4 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 7.9 in map P610L_Pre2-g1.mrc using 1292 points
correlation = 0.7418, correlation about mean = 0.4719, overlap = 447
steps = 80, shift = 5.22, angle = 16.3 degrees
Position of Pre0_p610l_EF-G.pdb map 7.9 (#41) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.97607139 0.12832321 -0.17554999 21.77681312
-0.09427392 0.97721736 0.19015433 -12.59378725
0.19595171 -0.16905441 0.96593143 -13.22856293
Axis -0.63840403 -0.66025169 -0.39561092
Axis point 87.49408480 0.00000000 110.83580532
Rotation angle (degrees) 16.33980178
Shift along axis -0.35397207
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #33.5 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_EF-G.pdb map 7.9 in map P610L_Pre2-g1.mrc using 967 points
correlation = 0.7642, correlation about mean = 0.5225, overlap = 352.6
steps = 72, shift = 1.41, angle = 6.16 degrees
Position of Pre0_p610l_EF-G.pdb map 7.9 (#42) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99897893 0.04134109 -0.01822106 -1.28922336
-0.03937154 0.99443872 0.09768064 -5.95488484
0.02215795 -0.09686351 0.99505100 6.33554353
Axis -0.90714153 -0.18828364 -0.37635556
Axis point 0.00000000 61.73927997 64.65842478
Rotation angle (degrees) 6.15561671
Shift along axis -0.09370163
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> fitmap #34 inMap #29 resolution 7.9 metric correlation
Fit map Pre0_p610l_ptRNA.pdb map 7.9 in map P610L_Pre2-g1.mrc using 2077
points
correlation = 0.7889, correlation about mean = 0.5454, overlap = 1293
steps = 56, shift = 1.22, angle = 3.57 degrees
Position of Pre0_p610l_ptRNA.pdb map 7.9 (#43) relative to P610L_Pre2-g1.mrc
(#29) coordinates:
Matrix rotation and translation
0.99821981 0.00921688 0.05892592 -14.94777255
-0.01027576 0.99979068 0.01769196 -1.59934734
-0.05875052 -0.01826598 0.99810557 12.74930998
Axis -0.28862865 0.94456997 -0.15646430
Axis point 210.90433222 0.00000000 256.08027058
Rotation angle (degrees) 3.57132439
Shift along axis 0.80884799
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> close #35-43
> hide #30 models
> hide #31 models
> hide #32 models
> hide #!33 models
> hide #34 models
> save Pre_p610l_30S.pdb models #30
> save Pre_p610l_50S.pdb models #31
> save Pre_p610l_atRNA.pdb models #32
> save Pre_p610l_EF-G.pdb models #33
> save Pre_p610l_ptRNA.pdb models #34
> show #30 models
> select #30/z
230 atoms, 255 bonds, 11 residues, 1 model selected
> save Pre_p610l_mRNA.pdb selectedOnly true
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G1/Pre2/Pre2_p610l_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G1/Pre2/Pre2_p610l_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
4 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 THR b 19 TYR b 21 1
3
Start residue of secondary structure not found: HELIX 2 2 PRO b 24 PHE b 29 1
6
Start residue of secondary structure not found: HELIX 3 3 LEU b 42 SER b 61 1
20
Start residue of secondary structure not found: HELIX 4 4 ARG b 73 SER b 85 1
13
Start residue of secondary structure not found: HELIX 5 5 TRP b 103 GLN b 121
1 19
156 messages similar to the above omitted
Chain information for Pre2_p610l_mRNA.pdb #35
---
Chain | Description
z | No description available
> hide #30 models
> hide #35 models
> select #30
52207 atoms, 56371 bonds, 4037 residues, 1 model selected
> volume zone #29 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #31
92129 atoms, 99979 bonds, 6860 residues, 1 model selected
> volume zone #29 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #33
5404 atoms, 5503 bonds, 697 residues, 6 models selected
> volume zone #29 nearAtoms sel range 4 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #32
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> volume zone #29 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #34
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> volume zone #29 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> select #35
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #29 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> save Pre_p610l_30S_range4.mrc models #36
> save Pre_p610l_50S_range4.mrc models #37
> save Pre_p610l_EF-G_range4.mrc models #38
> save Pre_p610l_atRNA_range3.mrc models #39
> save Pre_p610l_ptRNA_range3.mrc models #40
> hide #!41 models
> show #!41 models
> save Pre_p610l_mRNA_range3.mrc models #41
> close #30-32,34-35#33
> select #29-41
14 models selected
> volume sel & #!36-41 step 1
> volume sel level 3
> ui mousemode right select
> select clear
> ui mousemode right translate
> color #38 red
> color #40 deep sky blue
> color #41 green
> view 2
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/Figures/Pre2_P610L_topview.png"
> width 3000 height 4000 supersample 4
> hide #!36 models
> hide #!37 models
> hide #!38 models
> hide #!39 models
> hide #!40 models
> hide #!41 models
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G1/ChimeraX_sessions/Mutant_P610L_20201010.cxs"
> includeMaps true
> close #2-29,36-41
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and
> G3/temporary/presentation_20201013/Proj_G3/ChimeraX_sessions/test.cxs"
> includeMaps true
> close #1
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/pre0_j536_3d512_235A_sharpened.mrc"
Opened pre0_j536_3d512_235A_sharpened.mrc, grid size 512,512,512, pixel 0.652,
shown at level 5.08, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_30S.mrc"
Opened Pre0_wt_30S.mrc, grid size 512,512,512, pixel 0.652, shown at level
2.4, step 2, values float32
> hide #!2 models
> show #!2 models
> close #2
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_30S_range4.mrc"
Opened Pre0_wt_30S_range4.mrc, grid size 512,512,512, pixel 0.652, shown at
level 2.4, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_50S_range4.mrc"
Opened Pre0_wt_50S_range4.mrc, grid size 512,512,512, pixel 0.652, shown at
level 3.84, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1064+0+34 (frame:
1942x1120-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x532 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1120 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_atRNA_range3.mrc"
Opened Pre0_wt_atRNA_range3.mrc, grid size 512,512,512, pixel 0.652, shown at
level 4e-05, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1232+0+34 (frame:
1942x1288-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x616 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1288 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_mRNA_range3.mrc"
Opened Pre0_wt_mRNA_range3.mrc, grid size 512,512,512, pixel 0.652, shown at
level 0.000888, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1256+0+34 (frame:
1942x1312-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x628 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1312 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre0/Pre0_wt_ptRNA_range3.mrc"
Opened Pre0_wt_ptRNA_range3.mrc, grid size 512,512,512, pixel 0.652, shown at
level 0.00083, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/pre1_j620_3d288_44A_sharpened.mrc"
Opened pre1_j620_3d288_44A_sharpened.mrc, grid size 288,288,288, pixel 1.16,
shown at level 4, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_30S_range4.mrc"
Opened Pre1_wt_30S_range4.mrc, grid size 288,288,288, pixel 1.16, shown at
level 2.22, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_50S_range4.mrc"
Opened Pre1_wt_50S_range4.mrc, grid size 288,288,288, pixel 1.16, shown at
level 3.43, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_atRNA_range3.mrc"
Opened Pre1_wt_atRNA_range3.mrc, grid size 288,288,288, pixel 1.16, shown at
level 0.000689, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_mRNA_range3.mrc"
Opened Pre1_wt_mRNA_range3.mrc, grid size 288,288,288, pixel 1.16, shown at
level 0.00117, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre1/Pre1_wt_ptRNA_range3.mrc"
Opened Pre1_wt_ptRNA_range3.mrc, grid size 288,288,288, pixel 1.16, shown at
level 0.000114, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/pre2_j621_3d288_95A_sharpened.mrc"
Opened pre2_j621_3d288_95A_sharpened.mrc, 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_30S.mrc"
Opened Pre2_wt_30S.mrc, grid size 288,288,288, pixel 1.16, shown at level 2.7,
step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_50S.mrc"
Opened Pre2_wt_50S.mrc, 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_atRNA.mrc"
Opened Pre2_wt_atRNA.mrc, grid size 288,288,288, pixel 1.16, shown at level
0.00059, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_ptRNA.mrc"
Opened Pre2_wt_ptRNA.mrc, 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Pre2/Pre2_wt_mRNA.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2/Pre2_wt_mRNA.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
12 messages similar to the above omitted
Chain information for Pre2_wt_mRNA.pdb #18
---
Chain | Description
z | No description available
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!7 models
> hide #!9 models
> hide #!10 models
> hide #!12 models
> hide #!11 models
> show #!11 models
> hide #!13 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #18 models
> hide #!11 models
> hide #!14 models
> show #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #18 models
> hide #!14 models
> select #18
230 atoms, 255 bonds, 11 residues, 1 model selected
> volume zone #13 nearAtoms sel range 3 newMap true
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> hide #!19 models
> show #!19 models
> hide #18 models
> save Pre2_wt_mRNA_range3.mrc models #19
> close #18
> rename #19 id #18
> hide #!18 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc"
Opened pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc, grid size 512,512,512,
pixel 0.652, shown at level 4.33, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/Pre1_GDP-Pi_30S_range4.mrc"
Opened Pre1_GDP-Pi_30S_range4.mrc, grid size 512,512,512, pixel 0.652, shown
at level 2.21, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/Pre1_GDP-Pi_50S_range4.mrc"
Opened Pre1_GDP-Pi_50S_range4.mrc, 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/Pre1_GDP-Pi_atRNA_range3.mrc"
Opened Pre1_GDP-Pi_atRNA_range3.mrc, grid size 512,512,512, pixel 0.652, shown
at level 0.0013, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/Pre1_GDP-Pi_EF-G_range4.mrc"
Opened Pre1_GDP-Pi_EF-G_range4.mrc, 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/Pre1_GDP-Pi_mRNA_range3.mrc"
Opened Pre1_GDP-Pi_mRNA_range3.mrc, grid size 512,512,512, pixel 0.652, shown
at level 0.000387, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre1_GDP-
> Pi/Pre1_GDP-Pi_ptRNA_range3.mrc"
Opened Pre1_GDP-Pi_ptRNA_range3.mrc, grid size 512,512,512, pixel 0.652, shown
at level 0.00111, step 2, values float32
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/pre2_GDP-Pi_job918_3d512_36A_sharpened.mrc"
Opened pre2_GDP-Pi_job918_3d512_36A_sharpened.mrc, grid size 512,512,512,
pixel 0.652, shown at level 4.36, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1116+0+34 (frame:
1942x1172-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x986+0+34 (frame: 1942x1042-11-11) margins: 11, 45,
11, 11 minimum size: 288x558 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=598,1172 maxtrack=0,0)
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/Pre2_GDP-Pi_wt_30S_range4.mrc"
Opened Pre2_GDP-Pi_wt_30S_range4.mrc, grid size 512,512,512, pixel 0.652,
shown at level 2.63, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/Pre2_GDP-Pi_wt_50S_range4.mrc"
Opened Pre2_GDP-Pi_wt_50S_range4.mrc, grid size 512,512,512, pixel 0.652,
shown at level 3.75, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/Pre2_GDP-Pi_wt_atRNA_range3.mrc"
Opened Pre2_GDP-Pi_wt_atRNA_range3.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000597, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/Pre2_GDP-Pi_wt_EF-G_range4.mrc"
Opened Pre2_GDP-Pi_wt_EF-G_range4.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000695, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/Pre2_GDP-Pi_wt_mRNA_range3.mrc"
Opened Pre2_GDP-Pi_wt_mRNA_range3.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000778, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models Valik/Pre2_GDP-
> Pi/Pre2_GDP-Pi_wt_ptRNA_range3.mrc"
Opened Pre2_GDP-Pi_wt_ptRNA_range3.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000215, step 2, values float32
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> hide #!26 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc"
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc, 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/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/Chimeric_GDP1_wt_30S_range4.mrc"
Opened Chimeric_GDP1_wt_30S_range4.mrc, grid size 512,512,512, pixel 0.652,
shown at level 2.22, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/Chimeric_GDP1_wt_50S_range4.mrc"
Opened Chimeric_GDP1_wt_50S_range4.mrc, grid size 512,512,512, pixel 0.652,
shown at level 3.45, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/Chimeric_GDP1_wt_atRNA_range3.mrc"
Opened Chimeric_GDP1_wt_atRNA_range3.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000492, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/Chimeric_GDP1_wt_EF-G_range4.mrc"
Opened Chimeric_GDP1_wt_EF-G_range4.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000292, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/Chimeric_GDP1_wt_mRNA_range3.mrc"
Opened Chimeric_GDP1_wt_mRNA_range3.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000257, step 2, values float32
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/Models
> Valik/Chimeric_GDP1/Chimeric_GDP1_wt_ptRNA_range3.mrc"
Opened Chimeric_GDP1_wt_ptRNA_range3.mrc, grid size 512,512,512, pixel 0.652,
shown at level 0.000818, step 2, values float32
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> hide #!37 models
> hide #!38 models
> hide #!39 models
> select all
78 models selected
> volume sel level 3
> show #!1 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> hide #!1 models
> color #5 green
> show #!5 models
> hide #!5 models
> color #11 green
> color #18 green
> color #24 green
> color #31 green
> color #38 green
> show #!38 models
> hide #!38 models
> color #6 deep sky blue
> show #!6 models
> hide #!6 models
> color #12 deep sky blue
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> color #17 deep sky blue
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!24 models
> hide #!24 models
> color #25 deep sky blue
> show #!25 models
> hide #!25 models
> show #!31 models
> hide #!31 models
> color #32 deep sky blue
> show #!32 models
> hide #!32 models
> color #39 deep sky blue
> show #!39 models
> hide #!39 models
> color #23 red
> show #!23 models
> hide #!23 models
> color #30 red
> show #!30 models
> hide #!30 models
> color #37 red
> show #!37 models
> hide #!37 models
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/ChimeraX_sessions/Wild-
> type_partial_20201010.cxs" includeMaps true
opened ChimeraX session
> show #!33 models
> hide #!33 models
> show #!37 models
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/ChimeraX_pdbs/Wild-
> type/Chimeric_GDP1_wt_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/ChimeraX_pdbs/Wild-
type/Chimeric_GDP1_wt_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 426
END
1 messages similar to the above omitted
Chain information for Chimeric_GDP1_wt_EF-G.pdb #40
---
Chain | Description
x | No description available
> open "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/ChimeraX_pdbs/Wild-
> type/Pre2_GDP-Pi_wt_EF-G.pdb"
Summary of feedback from opening C:/Users/anasc/Documents/IMPRS -
Göttingen/Rotation 2 -Stark/Projects G1 and
G3/temporary/presentation_20201013/Proj_G3/ChimeraX_pdbs/Wild-type/Pre2_GDP-
Pi_wt_EF-G.pdb
---
warnings | Ignored bad PDB record found on line 414
END
Ignored bad PDB record found on line 417
END
Ignored bad PDB record found on line 420
END
Ignored bad PDB record found on line 423
END
Ignored bad PDB record found on line 5931
END
Start residue of secondary structure not found: HELIX 1 1 ARG 0 9 MET 0 14 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG 0 15 HIS 0 18 1
4
Start residue of secondary structure not found: HELIX 3 3 VAL 2 9 HIS 2 16 1 8
Start residue of secondary structure not found: HELIX 4 4 PHE 2 18 ALA 2 23 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS 2 25 LYS 2 37 1
13
406 messages similar to the above omitted
Chain information for Pre2_GDP-Pi_wt_EF-G.pdb #41
---
Chain | Description
x | No description available
> hide #!37 models
> hide #41 models
> hide #40 models
> show #41 models
> show #40 models
> show #!37 models
> hide #!37 models
> show #!33 models
> transparency #33 60
> ui tool show "Side View"
> hide #40 models
> show #40 models
> hide #!33 models
> hide #40 models
> show #!30 models
> show #!37 models
> show #40 models
> hide #40 models
> hide #!37 models
> hide #!30 models
> show #40 models
> hide #40 models
> show #!33 models
> hide #!33 models
> show #!33 models
> view 2
> hide #41 models
> view 2
> hide #!33 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!23 models
> show #!30 models
> show #!37 models
> view 2
> show #!10 models
> show #!12 models
> hide #!10 models
> show #!10 models
> hide #!4 models
> hide #!6 models
> show #!16 models
> hide #!16 models
> volume #1 step 1
> volume #10 step 1
> volume #12 step 1
> volume #12 level 2.5
> volume #12 level 2.4
> volume #12 level 2.5
> volume #10 level 2.5
> select all
10936 atoms, 11140 bonds, 1410 residues, 80 models selected
> volume sel & #!2-3,5,10,12,23,30,37 step 1
> ui mousemode right select
> select clear
> ui mousemode right translate
> hide #!30 models
> hide #!37 models
> hide #!23 models
> volume #4 step 1
> select all
10936 atoms, 11140 bonds, 1410 residues, 80 models selected
> volume sel & #!2-3,5,10,12 step 1
> volume sel & #!2-3,5,10,12 step 1
> ui mousemode right select
> select clear
> ui mousemode right translate
> volume #7 step 1
> volume #8 step 1
> volume #9 step 1
> volume #11 step 1
> volume #13 step 1
> volume #14 step 1
> volume #15 step 1
> volume #16 step 1
> volume #17 step 1
> volume #18 step 1
> volume #19 step 1
> volume #20 step 1
> volume #21 step 1
> volume #22 step 1
> volume #24 step 1
> volume #26 step 1
> volume #27 step 1
> volume #28 step 1
> volume #29 step 1
> volume #31 step 1
> volume #32 step 1
> volume #34 step 1
> volume #35 step 1
> volume #36 step 1
> volume #38 step 1
> volume #39 step 1
> volume #33 step 1
> volume #25 step 1
> volume #6 step 1
> hide #!10 models
> hide #!12 models
> hide #!5 models
> hide #!3 models
> hide #!21 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> volume #9 level 2.5
> volume #9 level 2.7
> volume #9 level 3
> volume #11 level 2.5
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!12 models
> volume #11 level 3
> volume #11 level 2.5
> volume #11 level 2
> volume #11 level 2.5
> show #!10 models
> show #!9 models
> show #!8 models
> show #!12 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> show #!14 models
> show #!15 models
> show #!16 models
> show #!17 models
> volume #16 level 2.5
> volume #16 level 2
> volume #17 level 2
> volume #18 level 2
> hide #!17 models
> hide #!16 models
> volume #18 level 2.5
> volume #18 level 2
> show #!17 models
> show #!16 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> show #!20 models
> show #!21 models
> show #!22 models
> show #!23 models
> show #!24 models
> show #!25 models
> volume #23 level 3.5
> volume #23 level 2.5
> volume #23 level 2
> volume #23 level 2.5
> volume #23 level 2.7
> volume #23 level 2.5
> volume #23 level 2.7
> hide #!25 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> hide #!21 models
> hide #!20 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
> show #!32 models
> volume #29 level 2.5
> volume #29 level 2
> volume #29 level 2.3
> volume #29 level 2.5
> volume #29 level 2.3
> volume #32 level 2.3
> volume #31 level 2.3
> volume #30 level 2.5
> volume #30 level 2.3
> volume #30 level 2
> volume #30 level 2.3
> volume #30 level 2.2
> volume #30 level 2
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> show #!34 models
> show #!35 models
> show #!36 models
> show #!37 models
> show #!38 models
> show #!39 models
> close #40-41
> volume #36 level 2.5
> volume #36 level 2.3
> volume #38 level 2.3
> volume #39 level 2.3
> save "C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/Projects
> G1 and G3/temporary/presentation_20201013/Proj_G3/ChimeraX_sessions/Wild-
> type_partial_20201011.cxs" includeMaps true
opened ChimeraX session
> hide #!39 models
> hide #!38 models
> hide #!37 models
> hide #!36 models
> hide #!35 models
> hide #!34 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> view 2
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> show #!14 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #!10 models
> show #!12 models
> hide #!12 models
> hide #!10 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> show #!20 models
> show #!21 models
> show #!22 models
> hide #!22 models
> hide #!21 models
> view 2
> show #!21 models
> show #!22 models
> show #!23 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> hide #!21 models
> hide #!20 models
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
> show #!32 models
> volume #30 level 2.5
> volume #30 level 2.3
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!30 models
> show #!30 models
> hide #!23 models
> volume #30 level 2.4
> volume #30 level 2.3
> hide #!27 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!32 models
> show #!35 models
> show #!36 models
> show #!34 models
> hide #!35 models
> hide #!36 models
> show #!35 models
> show #!36 models
> show #!37 models
> show #!38 models
> show #!39 models
> show #!33 models
> hide #!39 models
> hide #!38 models
> hide #!37 models
> hide #!35 models
> hide #!34 models
> select #33
2 models selected
> color sel #0054fd
> show #!34 models
> hide #!33 models
> show #!33 models
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\view.py", line 165, in draw
self._draw_scene(camera, drawings)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\view.py", line 240, in _draw_scene
draw_transparent(r, transparent_drawings)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1493, in draw_transparent
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1169, in draw_transparent
draw_depth()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1492, in <lambda>
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DEPTH_DRAW_PASS),
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1499, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 739, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 750, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 773, in _draw_geometry
ds.activate_bindings(renderer)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1846, in activate_bindings
self.update_buffers()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1834, in update_buffers
b.update_buffer_data(data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 2599, in update_buffer_data
d = data.astype(self.value_type, order = 'C')
MemoryError: Unable to allocate 78.7 MiB for an array with shape (6878516, 3)
and data type uint32
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 18362)
Memory: 8,356,519,936
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unable to allocate buffer |
comment:2 by , 5 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
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This ChimeraX simply says your computer did not have enough memory. It was trying to make some graphics like a map surface or atomic model ribbon.
MemoryError: Unable to allocate 78.7 MiB for an array with shape (6878516, 3) and data type uint32
It was only trying to allocate 78.7 Mbytes -- it was not trying to allocate a huge amount.
I see you have many 512x512x512 maps open and 40 models opened at the same time, and your computer has only 8 Gbytes of memory. That is too little memory to work with large data. Typical computer memory these days is 16 Gbytes, and for working with larger data I would recommend 32 Gbytes.
It is possible that as you open and close lots of data sets ChimeraX may not release the memory due to a bug. The Python language automatically releases the memory only when none of the code holds a reference to it, and sometimes references are held even after the data is closed. To minimize that problem, instead of closing 30 models and opening 30 new ones, you might want to quit ChimeraX and start it again.
If you think it is a memory leak where ChimeraX is not releasing memory I would need some test case to reproduce that. You could watch the memory use of ChimeraX as you open and close data and perhaps see where ChimeraX is not releasing the memory, and use Help / Report a Bug so I can see an exact log of what steps you took so I could figure out what tool in ChimeraX might be holding references to closed data.