add_modified() not handling sets

[sitins07@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open X:/Work/Projects/EF-G/g3/finalmaps/All_models.cxs

Opened pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc as #1.2, grid size
512,512,512, pixel 0.652, shown at level 3, step 1, values float32  
Opened pre1_GDP-Pi-1_job1482_4A_sharpened.mrc as #2.2, grid size 288,288,288,
pixel 1.16, shown at level 3, step 1, values float32  
Opened pre1_GDP-Pi-2_job1455_68A_sharpened.mrc as #3.2, grid size 288,288,288,
pixel 1.16, shown at level 3, step 1, values float32  
Opened pre1_GDP-Pi-3_job1454_59A_sharpened.mrc as #4.2, grid size 288,288,288,
pixel 1.16, shown at level 4.42, step 2, values float32  
Opened pre1_GDP_job788_51A_sharpened.mrc as #5.2, grid size 288,288,288, pixel
1.16, shown at level 4.19, step 2, values float32  
Opened pre2_GDP-Pi_job918_3d512_36A_sharpened.mrc as #6.2, grid size
512,512,512, pixel 0.652, shown at level 4.36, step 2, values float32  
Opened pre2_GDP-Pi-1_job998_44A_sharpened.mrc as #7.2, grid size 288,288,288,
pixel 1.16, shown at level 4.01, step 2, values float32  
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #8.2, grid size
512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32  
Opened chimeric_GDP1-1_job1131_6A_sharpened.mrc as #8.4, grid size
288,288,288, pixel 1.16, shown at level 2.5, step 2, values float32  
Opened chimeric_GDP2_job914_44A_sharpened.mrc as #9.2, grid size 288,288,288,
pixel 1.16, shown at level 3, step 1, values float32  
Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #10.2, grid size
512,512,512, pixel 0.652, shown at level 5.08, step 2, values float32  
Opened h1_j620_3d288_44A_sharpened.mrc as #11.2, grid size 288,288,288, pixel
1.16, shown at level 4, step 2, values float32  
Opened h2_j621_3d288_95A_sharpened.mrc as #12.2, grid size 288,288,288, pixel
1.16, shown at level 4.17, step 2, values float32  
Log from Sun Nov 15 16:36:39 2020UCSF ChimeraX version: 1.2.dev202011070209
(2020-11-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home/vpetryc/projects/data_share_Niels/g3/All_current_states.cxs

Log from Fri Nov 13 02:11:05 2020UCSF ChimeraX version: 1.2.dev202011070209
(2020-11-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home/vpetryc/projects/translocation/g3/All_models.cxs format session

Log from Mon Nov 9 17:30:56 2020UCSF ChimeraX version: 1.2.dev202011070209
(2020-11-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi/models/Pre-1_v4.5-coot-31.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP-
Pi/models/Pre-1_v4.5-coot-31.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3146 )  
54 messages similar to the above omitted  
  
Chain information for Pre-1_v4.5-coot-31.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  
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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  
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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  
  

> style stick

Changed 153093 atom styles  

> show cartoons

> hide atoms

> select /x:1-702

5436 atoms, 5538 bonds, 702 residues, 1 model selected  

> sequence chain #1/x

Alignment identifier is 1/x  

> close #1

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi/models/Pre-1_v4.5-coot-31.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP-
Pi/models/Pre-1_v4.5-coot-31.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3146 )  
54 messages similar to the above omitted  
  
Chain information for Pre-1_v4.5-coot-31.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  
x | No description available  
y | No description available  
z | No description available  
  

> hide atoms

> show cartoons

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi/models/Pre-1_v4.5-coot-31.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP-
Pi/models/Pre-1_v4.5-coot-31.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3146 )  
54 messages similar to the above omitted  
  
Chain information for Pre-1_v4.5-coot-31.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi/models/Pre-1_v4.5-coot-31.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP-
Pi/models/Pre-1_v4.5-coot-31.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3146 )  
54 messages similar to the above omitted  
  
Chain information for Pre-1_v4.5-coot-31.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> close #1-2

> show cartoons

> hide atoms

> close #3

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi/models/Pre1_GDP-
> Pi_RSR-4-coot-32.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP-Pi/models/Pre1_GDP-
Pi_RSR-4-coot-32.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3146 )  
54 messages similar to the above omitted  
  
Chain information for Pre1_GDP-Pi_RSR-4-coot-32.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  
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J | No description available  
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L | No description available  
M | No description available  
N | No description available  
O | No description available  
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S | No description available  
T | No description available  
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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  
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f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide atoms

> hide cartoons

> show cartoons

> style stick

Changed 153093 atom styles  

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi/sharpened/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  

> rename #1-2 id 1

> rename #1 Pre1_GDP-Pi

> save /home/vpetryc/projects/translocation/g3/All_models.cxs includeMaps true

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-1/models/Pre1_GDP-
> Pi-1_RSR-1-coot-2.pdb

Chain information for Pre1_GDP-Pi-1_RSR-1-coot-2.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
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S | No description available  
T | No description available  
U | No description available  
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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  
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h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!1 models

> show #!2 cartoons

> hide #!2 atoms

> close #2

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-1/models/Pre1_GDP-
> Pi-1_RSR-1-coot-2.pdb

Chain information for Pre1_GDP-Pi-1_RSR-1-coot-2.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
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W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
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i | No description available  
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l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 cartoons

> hide #!2 atoms

> show #!2 cartoons

> close #2

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi-1/sharpened/pre1_GDP-Pi-1_job1482_4A_sharpened.mrc

Opened pre1_GDP-Pi-1_job1482_4A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 4.05, step 2, values float32  

> close #2

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-1/models/Pre1_GDP-
> Pi-1_RSR-1-coot-2.pdb

Chain information for Pre1_GDP-Pi-1_RSR-1-coot-2.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> show #2 cartoons

> select #2

153093 atoms, 165586 bonds, 11761 residues, 1 model selected  

> hide sel atoms

> ui mousemode right select

> select clear

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi-1/sharpened/pre1_GDP-Pi-1_job1482_4A_sharpened.mrc

Opened pre1_GDP-Pi-1_job1482_4A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 4.05, step 2, values float32  

> volume #!3 step 1

> volume #1.2 step 1

> volume level 2

> volume level 3

> select

306186 atoms, 331172 bonds, 775 pseudobonds, 23522 residues, 9 models selected  

> select clear

> select #2@mg

370 atoms, 370 residues, 1 model selected  

> delete sel

> save /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-1/models/Pre1_GDP-
> Pi-1_RSR-1-coot-3.pdb models #2

> close #2

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-1/models/Pre1_GDP-
> Pi-1_RSR-1-coot-4.pdb

Chain information for Pre1_GDP-Pi-1_RSR-1-coot-4.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #2 atoms

> show #2 cartoons

> show #!3 models

> rename #2-3 id 2

> rename #1 Pre1_GDP-Pi-1

> rename #1 Pre1_GDP-Pi

> rename #2 Pre1_GDP-Pi-1

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2.2 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!2 models

> hide #!1 models

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-2/models/Pre1_GDP-
> Pi-2_RSR-1-coot-1.pdb

Chain information for Pre1_GDP-Pi-2_RSR-1-coot-1.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!3 atoms

> show #!3 cartoons

> select #3@mg

370 atoms, 1 pseudobond, 370 residues, 2 models selected  

> delete sel

> save /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-2/models/Pre1_GDP-
> Pi-2_RSR-1-coot-2.pdb models #3

> close #3

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-2/models/Pre1_GDP-
> Pi-2_RSR-1-coot-2.pdb

Chain information for Pre1_GDP-Pi-2_RSR-1-coot-2.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!3 atoms

> show #!3 cartoons

> close #3

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-2/models/Pre1_GDP-
> Pi-2_RSR-1-coot-2.pdb

Chain information for Pre1_GDP-Pi-2_RSR-1-coot-2.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #3 atoms

> show #3 cartoons

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi-2/sharpened/pre1_GDP-Pi-2_job1455_68A_sharpened.mrc

Opened pre1_GDP-Pi-2_job1455_68A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 4.35, step 2, values float32  

> rename #3-4 id 3

> rename #3 Pre1_GDP-Pi-2

> volume #3.2 step 1

> volume #3.2 level 3

> hide #!3 models

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-3/models/Pre1_GDP-
> Pi-3_RSR-1-coot-1.pdb

Chain information for Pre1_GDP-Pi-3_RSR-1-coot-1.pdb #4  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!4 atoms

> show #!4 cartoons

> select #4@mg

370 atoms, 1 pseudobond, 370 residues, 2 models selected  

> delete sel

> save /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-3/models/Pre1_GDP-
> Pi-3_RSR-1-coot-2.pdb models #4

> close #4

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-3/models/Pre1_GDP-
> Pi-3_RSR-1-coot-2.pdb

Chain information for Pre1_GDP-Pi-3_RSR-1-coot-2.pdb #4  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #4 atoms

> show #4 cartoons

> close #4

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi-3/models/Pre1_GDP-
> Pi-3_RSR-1-coot-3.pdb

Chain information for Pre1_GDP-Pi-3_RSR-1-coot-3.pdb #4  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-
> Pi-3/sharpened/pre1_GDP-Pi-3_job1454_59A_sharpened.mrc

Opened pre1_GDP-Pi-3_job1454_59A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 4.42, step 2, values float32  

> rename #4-5 id 4

> rename #4 Pre1_GDP-Pi-3

> hide #!4 models

> save /home/vpetryc/projects/translocation/g3/All_models.cxs includeMaps true

——— End of log from Mon Nov 9 17:30:56 2020 ———

opened ChimeraX session  

> open
> /home/vpetryc/projects/translocation/g3/pre1_GDP/models/Pre1_GDP_RSR-0-coot-2.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP/models/Pre1_GDP_RSR-0-coot-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 196 196 TYR x
548 GLY x 563 1 16  
Start residue of secondary structure not found: HELIX 197 197 SER x 588 LYS x
608 1 21  
Start residue of secondary structure not found: HELIX 201 201 SER x 691 GLY x
702 1 12  
Start residue of secondary structure not found: SHEET 1 224 1 ALA x 488 GLU x
491 0  
Start residue of secondary structure not found: SHEET 1 225 1 VAL x 497 LYS x
506 0  
6 messages similar to the above omitted  
  
Chain information for Pre1_GDP_RSR-0-coot-2.pdb #5  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open
> /home/vpetryc/projects/translocation/g3/pre1_GDP/sharpened/pre1_GDP_job788_51A_sharpened.mrc

Opened pre1_GDP_job788_51A_sharpened.mrc, grid size 288,288,288, pixel 1.16,
shown at level 4.19, step 2, values float32  

> rename #5-6 id 5

> rename #5 Pre1_GDP

> hide #!5 models

> open /home/vpetryc/projects/translocation/g3/pre2_GDP-Pi/models/Pre2_GDP-
> Pi_RSR-0-coot-6.pdb

Chain information for Pre2_GDP-Pi_RSR-0-coot-6.pdb #6  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> show #!6 cartoons

> hide #!6 atoms

> open /home/vpetryc/projects/translocation/g3/pre2_GDP-Pi/sharpened/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  

> rename #6-7 id 6

> rename #6 Pre2_GDP-Pi

> hide #!6 models

> open /home/vpetryc/projects/translocation/g3/pre2_GDP-Pi-1/models/Pre2_GDP-
> Pi-1_RSR-0-coot-3.pdb

Chain information for Pre2_GDP-Pi-1_RSR-0-coot-3.pdb #7  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!7 atoms

> show #!7 cartoons

> open /home/vpetryc/projects/translocation/g3/pre2_GDP-
> Pi-1/sharpened/pre2_GDP-Pi-1_job998_44A_sharpened.mrc

Opened pre2_GDP-Pi-1_job998_44A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 4.01, step 2, values float32  

> rename #7-8 id 7

> rename #7 Pre2_GDP-Pi-1

> hide #!7 models

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP1/General/models/Chimeric_GDP-1-RSR-0-coot-2.pdb

Chain information for Chimeric_GDP-1-RSR-0-coot-2.pdb #8  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #8 atoms

> show #8 cartoons

> select #8/w:1

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #8/w:1

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /v:101

10 atoms, 9 bonds, 1 residue, 1 model selected  

> show sel atoms

> delete sel

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP1/General/sharpened/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  

> rename #8-9 id 8

> rename #8 Chimeric_GDP-1

> hide #!8 models

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP1/General/Chimeric_GDP-
> sw1.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/chimeric_GDP1/General/Chimeric_GDP-
sw1.pdb  
---  
warning | Ignored bad PDB record found on line 261411  
END  
  
Chain information for Chimeric_GDP-sw1.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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!9 atoms

> show #!9 cartoons

> rename #9 id 8.3

> show #!8 models

> hide #8.1 models

> hide #!8.3 models

> volume #8.2 step 1

> volume #8.2 level 2.5

> show #8.1 models

> hide #8.1 models

> show #!8.3 models

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP1/switch1_substates/chimeric_GDP1-1_job1131_6A_sharpened.mrc

Opened chimeric_GDP1-1_job1131_6A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 4.51, step 2, values float32  

> volume #9 level 2.5

> rename #9 id 8.4

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP2/models/Chimeric_GDP-2-RSR-0-coot-2.pdb

Chain information for Chimeric_GDP-2-RSR-0-coot-2.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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!8 models

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP2/sharpened/chimeric_GDP2_job914_44A_sharpened.mrc

Opened chimeric_GDP2_job914_44A_sharpened.mrc, grid size 288,288,288, pixel
1.16, shown at level 3.99, step 2, values float32  

> hide #9 atoms

> show #9 cartoons

> volume #10 level 2

> volume #10 step 1

> volume #10 level 3

> rename #9-10 id 9

> rename #9 Chimeric_GDP-2

> open
> /home/vpetryc/projects/translocation/g3/70S_tRNA/70S_APa_v0.1-6-coot-44.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/70S_tRNA/70S_APa_v0.1-6-coot-44.pdb  
---  
warnings | Ignored bad PDB record found on line 149636  
END  
  
Start residue of secondary structure not found: HELIX 195 195 ASP s 11 SER s
24 1 14  
Start residue of secondary structure not found: HELIX 196 196 LYS s 69 PRO s
75 1 7  
Start residue of secondary structure not found: SHEET 1 233 1 PRO s 29 TRP s
33 0  
Start residue of secondary structure not found: SHEET 1 234 1 LEU s 46 HIS s
51 0  
Start residue of secondary structure not found: SHEET 1 235 1 HIS s 56 VAL s
61 0  
  
Chain information for 70S_APa_v0.1-6-coot-44.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  
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  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
y | No description available  
z | No description available  
  

> close #10

> open /home/vpetryc/projects/translocation/g3/70S_tRNA/70S_AP_v2.cif-
> coot-2.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/70S_tRNA/70S_AP_v2.cif-coot-2.pdb  
---  
warning | Ignored bad PDB record found on line 147610  
END  
  
Chain information for 70S_AP_v2.cif-coot-2.pdb #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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
y | No description available  
z | No description available  
  

> hide #!9 models

> hide #10 atoms

> show #10 cartoons

> open
> /home/vpetryc/projects/translocation/g3/70S_tRNA/70S_APtRNA_job536_3d512_235A_sharpened_a.mrc

Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc, grid size 512,512,512,
pixel 0.652, shown at level 5.08, step 2, values float32  

> rename #10-11 id 10

> rename #10 70S_AP

> hide #!10 models

> open
> /home/vpetryc/projects/translocation/g3/70S_hybridtRNA_1/70S_tRNA_c1_real_space_refined.pdb
> /home/vpetryc/projects/translocation/g3/70S_hybridtRNA_1/h1_j620_3d288_44A_sharpened.mrc

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/70S_hybridtRNA_1/70S_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  
  
Opened h1_j620_3d288_44A_sharpened.mrc, grid size 288,288,288, pixel 1.16,
shown at level 4, step 2, values float32  

> rename #11-12 id 11

> rename #11 70S_hybrid-1

> hide #!11 models

> open
> /home/vpetryc/projects/translocation/g3/70S_hybridtRNA_2/70S_tRNA_c2_real_space_refined.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/70S_hybridtRNA_2/70S_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 #12  
---  
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  
  

> show #!12 cartoons

> hide #!12 atoms

> open
> /home/vpetryc/projects/translocation/g3/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc

Opened h2_j621_3d288_95A_sharpened.mrc, grid size 288,288,288, pixel 1.16,
shown at level 4.17, step 2, values float32  

> rename #12-13 id 12

> rename #12 70S_hybrid-2

> save /home/vpetryc/projects/data_share_Niels/g3/All_current_states.cxs
> includeMaps true

——— End of log from Fri Nov 13 02:11:05 2020 ———

opened ChimeraX session  

> save /home/aschwar1/projects/g3/All_current.cxs includeMaps true

> open
> /home/vpetryc/projects/translocation/g3/70S_hybridtRNA_1/70S_tRNA_c1_RSR-1-coot-4.pdb

Chain information for 70S_tRNA_c1_RSR-1-coot-4.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  
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
> /home/vpetryc/projects/translocation/g3/70S_hybridtRNA_1/70S_tRNA_c2_RSR-1-coot-2.pdb

Chain information for 70S_tRNA_c2_RSR-1-coot-2.pdb #14  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
y | No description available  
z | No description available  
  

> hide #!12 models

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP1/General/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb

Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb #15  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #!13 models

> hide #!14 models

> hide #15 atoms

> show #15 cartoons

> open
> /home/vpetryc/projects/translocation/g3/chimeric_GDP1/General/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb

Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb #16  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #16 models

> open /home/vpetryc/projects/translocation/g3/pre1_GDP-Pi/models/Pre1_GDP-
> Pi_RSR-4-coot-32.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP-Pi/models/Pre1_GDP-
Pi_RSR-4-coot-32.pdb  
---  
warnings | Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3061 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3078 )  
Cannot find LINK/SSBOND residue MG (3146 )  
54 messages similar to the above omitted  
  
Chain information for Pre1_GDP-Pi_RSR-4-coot-32.pdb #17  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #15#!17 atoms

> show #15#!17 cartoons

> mmaker #16/a to #10/a matrix Nuclein

> matchmaker #16/a to #10/a matrix Nuclein

Invalid "matrix" argument: Should be one of 'BLOSUM-100', 'BLOSUM-30',
'BLOSUM-35', 'BLOSUM-40', 'BLOSUM-45', 'BLOSUM-50', 'BLOSUM-55', 'BLOSUM-60',
'BLOSUM-62', 'BLOSUM-65', 'BLOSUM-70', 'BLOSUM-75', 'BLOSUM-80', 'BLOSUM-85',
'BLOSUM-90', 'BLOSUM-N', 'Grantham', 'HSDM', 'Nucleic', 'PAM-120', 'PAM-150',
'PAM-250', 'PAM-40', or 'SDM'  

> mmaker #16/a to #10/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain a (#10.1) with
Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain a (#16), sequence alignment
score = 6144.6  
RMSD between 1004 pruned atom pairs is 0.727 angstroms; (across all 1540
pairs: 7.961)  
  

> mmaker #17/a to #10/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain a (#10.1) with Pre1_GDP-
Pi_RSR-4-coot-32.pdb, chain a (#17), sequence alignment score = 6144.6  
RMSD between 1170 pruned atom pairs is 0.667 angstroms; (across all 1540
pairs: 2.103)  
  

> mmaker #17/a to #16/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain a (#16) with
Pre1_GDP-Pi_RSR-4-coot-32.pdb, chain a (#17), sequence alignment score =
6144.6  
RMSD between 1005 pruned atom pairs is 0.758 angstroms; (across all 1540
pairs: 5.992)  
  

> hide #15 models

> show #16 models

> hide #16#!17 atoms

> show #16#!17 cartoons

> ui mousemode right select

> select #17/x:679

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 47 bonds, 6 residues, 1 model selected  

> select up

5480 atoms, 5581 bonds, 707 residues, 1 model selected  

> color sel red

> select #16/x:155

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

102 atoms, 102 bonds, 12 residues, 1 model selected  

> select up

5473 atoms, 5576 bonds, 704 residues, 1 model selected  

> select up

153027 atoms, 165562 bonds, 11713 residues, 1 model selected  

> select down

5473 atoms, 5576 bonds, 704 residues, 1 model selected  

> color sel yellow

> select clear

> open
> /home/vpetryc/projects/translocation/g3/pre1_GDP/models/Pre1_GDP_RSR-0-coot-2.pdb

Summary of feedback from opening
/home/vpetryc/projects/translocation/g3/pre1_GDP/models/Pre1_GDP_RSR-0-coot-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 196 196 TYR x
548 GLY x 563 1 16  
Start residue of secondary structure not found: HELIX 197 197 SER x 588 LYS x
608 1 21  
Start residue of secondary structure not found: HELIX 201 201 SER x 691 GLY x
702 1 12  
Start residue of secondary structure not found: SHEET 1 224 1 ALA x 488 GLU x
491 0  
Start residue of secondary structure not found: SHEET 1 225 1 VAL x 497 LYS x
506 0  
6 messages similar to the above omitted  
  
Chain information for Pre1_GDP_RSR-0-coot-2.pdb #18  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide #16#!17-18 atoms

> show #16#!17-18 cartoons

> mmaker #18/a to #10/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain a (#10.1) with
Pre1_GDP_RSR-0-coot-2.pdb, chain a (#18), sequence alignment score = 6144.6  
RMSD between 1170 pruned atom pairs is 0.667 angstroms; (across all 1540
pairs: 2.103)  
  

> hide #!17 models

> hide #16 models

> show #!17 models

> show #16 models

> select #18/x:253

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

126 atoms, 125 bonds, 16 residues, 1 model selected  

> select up

4325 atoms, 4399 bonds, 555 residues, 1 model selected  

> color sel orange

> select clear

> select #16-17/x:338,356,358,361,37

110 atoms, 104 bonds, 10 residues, 2 models selected  

> show sel atoms

> ui mousemode right pivot

> style sel stick

Changed 110 atom styles  

> select #16-17/x:328,356,358,361,37

108 atoms, 102 bonds, 10 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 108 atom styles  

> select #16-17/x:328,356,358,361,37 /a:55

152 atoms, 150 bonds, 12 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 152 atom styles  

> select #17/x:358

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #16-17/x:328,356,358,361,37 /a:55

152 atoms, 150 bonds, 12 residues, 2 models selected  

> style sel ball

Changed 152 atom styles  

> color sel byhetero

> ui mousemode right select

> select #17/X:54

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> hide #!18 models

> mmaker #17/x to #16/x matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain A (#16) with
Pre1_GDP-Pi_RSR-4-coot-32.pdb, chain A (#17), sequence alignment score = 0  
Fewer than 3 residues aligned; cannot match
Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain A with Pre1_GDP-
Pi_RSR-4-coot-32.pdb, chain A  

> mmaker #17/x to #16/x

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain x (#16) with
Pre1_GDP-Pi_RSR-4-coot-32.pdb, chain x (#17), sequence alignment score =
3108.4  
RMSD between 555 pruned atom pairs is 1.114 angstroms; (across all 702 pairs:
6.141)  
  

> ui mousemode right pivot

> ui mousemode right select

> select #16/x:577

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

57 atoms, 57 bonds, 7 residues, 1 model selected  

> select up

5473 atoms, 5576 bonds, 704 residues, 1 model selected  

> select up

153027 atoms, 165562 bonds, 11713 residues, 1 model selected  

> color sel orange

> select down

5473 atoms, 5576 bonds, 704 residues, 1 model selected  

> color sel red orange

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel red-orange

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel darkorange

> color sel dimorange

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel red

> select #17/x:554

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

121 atoms, 122 bonds, 16 residues, 1 model selected  

> select up

5480 atoms, 5581 bonds, 707 residues, 1 model selected  

> color sel yellow

> select clear

> mmaker #17/a to #16/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain a (#16) with
Pre1_GDP-Pi_RSR-4-coot-32.pdb, chain a (#17), sequence alignment score =
6144.6  
RMSD between 1005 pruned atom pairs is 0.758 angstroms; (across all 1540
pairs: 5.992)  
  

> save /home/vpetryc/projects/translocation/g3/All_models.cxs includeMaps true

——— End of log from Sun Nov 15 16:36:39 2020 ———

opened ChimeraX session  

> select #10.1/A

62599 atoms, 69818 bonds, 3164 residues, 1 model selected  

> molmap sel 3

Opened 70S_AP_v2.cif-coot-2.pdb map 3 as #19, grid size 210,202,212, pixel 1,
shown at level 0.141, step 1, values float32  

> mmaker #1.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with Pre1_GDP-
Pi_RSR-4-coot-32.pdb, chain A (#1.1), sequence alignment score = 11579.8  
RMSD between 2721 pruned atom pairs is 0.483 angstroms; (across all 2903
pairs: 3.598)  
  

> hide #!17 models

> hide #16 models

> show #!1 models

> show #!1.2 models

> fitmap #1.2 inMap #19

Fit map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc in map 70S_AP_v2.cif-
coot-2.pdb map 3 using 2630225 points  
correlation = 0.6721, correlation about mean = 0.4042, overlap = 5.58e+06  
steps = 132, shift = 0.83, angle = 3.01 degrees  
  
Position of pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc (#1.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99920374 -0.00294244 -0.03978978 7.13467338  
0.00430402 0.99940652 0.03417711 -6.50523777  
0.03966561 -0.03432115 0.99862340 0.03518193  
Axis -0.65139965 -0.75559887 0.06891184  
Axis point 5.95490019 -0.00000000 183.61429873  
Rotation angle (degrees) 3.01387328  
Shift along axis 0.27025105  
  

> hide #!1 models

> show #!2 models

> show #!2.2 models

> fitmap #2.2 inMap #19

Fit map pre1_GDP-Pi-1_job1482_4A_sharpened.mrc in map 70S_AP_v2.cif-coot-2.pdb
map 3 using 441358 points  
correlation = 0.6289, correlation about mean = 0.3045, overlap = 7.788e+05  
steps = 104, shift = 0.61, angle = 3.26 degrees  
  
Position of pre1_GDP-Pi-1_job1482_4A_sharpened.mrc (#2.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99897419 0.00090420 -0.04527427 7.51111698  
0.00065441 0.99940796 0.03439924 -5.92761026  
0.04527857 -0.03439358 0.99838216 -1.05862210  
Axis -0.60492942 -0.79627606 -0.00219648  
Axis point 29.36089331 0.00000000 167.62422812  
Rotation angle (degrees) 3.25960796  
Shift along axis 0.17864373  
  

> mmaker #2.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with Pre1_GDP-
Pi-1_RSR-1-coot-4.pdb, chain A (#2.1), sequence alignment score = 11579.8  
RMSD between 2712 pruned atom pairs is 0.565 angstroms; (across all 2903
pairs: 3.609)  
  

> hide #!2 models

> show #!3 models

> show #!3.2 models

> mmaker #3.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with Pre1_GDP-
Pi-2_RSR-1-coot-2.pdb, chain A (#3.1), sequence alignment score = 11579.8  
RMSD between 2670 pruned atom pairs is 0.693 angstroms; (across all 2903
pairs: 3.678)  
  

> fitmap #3.2 inMap #19

Fit map pre1_GDP-Pi-2_job1455_68A_sharpened.mrc in map 70S_AP_v2.cif-
coot-2.pdb map 3 using 610074 points  
correlation = 0.5748, correlation about mean = 0.1628, overlap = 7.739e+05  
steps = 128, shift = 0.619, angle = 1.96 degrees  
  
Position of pre1_GDP-Pi-2_job1455_68A_sharpened.mrc (#3.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99963492 -0.00005365 -0.02701907 4.45725727  
0.00061776 0.99978200 0.02087016 -3.66611120  
0.02701206 -0.02087923 0.99941703 -0.38603698  
Axis -0.61140021 -0.79126045 0.00983242  
Axis point 17.99281734 0.00000000 168.61345884  
Rotation angle (degrees) 1.95659822  
Shift along axis 0.17188509  
  

> hide #!3 models

> show #!4 models

> hide #4.1 atoms

> show #4.1 cartoons

> volume #4.2 step 1

> close #4.2

> open X:/Work/Projects/EF-G/g3/Final_Modelling/pre1_GDP-
> Pi-3/sharpened/pre1_GDP-Pi-3_job1454_59A_sharpened_b50.mrc

Opened pre1_GDP-Pi-3_job1454_59A_sharpened_b50.mrc as #20, grid size
288,288,288, pixel 1.16, shown at level 4.15, step 2, values float32  

> rename #20 id 4.2

> fitmap #4.2 inMap #19

Fit map pre1_GDP-Pi-3_job1454_59A_sharpened_b50.mrc in map 70S_AP_v2.cif-
coot-2.pdb map 3 using 29834 points  
correlation = 0.6482, correlation about mean = 0.09137, overlap = 5.617e+04  
steps = 76, shift = 0.595, angle = 3.24 degrees  
  
Position of pre1_GDP-Pi-3_job1454_59A_sharpened_b50.mrc (#4.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99898019 -0.00077810 -0.04514390 7.77171334  
0.00230752 0.99942472 0.03383645 -6.11867982  
0.04509160 -0.03390611 0.99840729 -1.06698071  
Axis -0.60014961 -0.79942052 0.02733637  
Axis point 29.93244823 0.00000000 174.11083799  
Rotation angle (degrees) 3.23538206  
Shift along axis 0.19804005  
  

> volume #6.2 step 1

> volume #6.2 level 3

> volume #6.2 level 2.816

> volume #4.2 step 1

> volume #4.2 level 3

> mmaker #4.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with Pre1_GDP-
Pi-3_RSR-1-coot-3.pdb, chain A (#4.1), sequence alignment score = 11579.8  
RMSD between 2691 pruned atom pairs is 0.610 angstroms; (across all 2903
pairs: 3.643)  
  

> hide #!4 models

> show #!5 models

> close #5.2

> hide #!5.1 atoms

> show #!5.1 cartoons

> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/pre1_GDP/sharpened/pre1_GDP_job788_6A_sharpened_b50.mrc

Opened pre1_GDP_job788_6A_sharpened_b50.mrc as #20, grid size 288,288,288,
pixel 1.16, shown at level 4.33, step 2, values float32  

> volume #20 step 1

> volume #20 level 3

> volume #20 level 1.823

> rename #20 id 5.2

> mmaker #5.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
Pre1_GDP_RSR-0-coot-2.pdb, chain A (#5.1), sequence alignment score = 11579.8  
RMSD between 2721 pruned atom pairs is 0.483 angstroms; (across all 2903
pairs: 3.598)  
  

> fitmap #5.2 inMap #19

Fit map pre1_GDP_job788_6A_sharpened_b50.mrc in map 70S_AP_v2.cif-coot-2.pdb
map 3 using 1427795 points  
correlation = 0.5413, correlation about mean = 0.339, overlap = 1.052e+06  
steps = 192, shift = 0.714, angle = 3.51 degrees  
  
Position of pre1_GDP_job788_6A_sharpened_b50.mrc (#5.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99859337 -0.01303899 -0.05139334 10.76106812  
0.01460379 0.99943747 0.03019060 -7.52755688  
0.05097078 -0.03089867 0.99822205 -2.47302574  
Axis -0.49921745 -0.83651264 0.22589497  
Axis point 57.51411337 0.00000000 211.36882382  
Rotation angle (degrees) 3.50783545  
Shift along axis 0.36613937  
  

> hide #!5 models

> show #!6.2 models

> fitmap #6.2 inMap #19

Fit map pre2_GDP-Pi_job918_3d512_36A_sharpened.mrc in map 70S_AP_v2.cif-
coot-2.pdb map 3 using 3539745 points  
correlation = 0.6239, correlation about mean = 0.3414, overlap = 5.311e+06  
steps = 80, shift = 0.788, angle = 2.71 degrees  
  
Position of pre2_GDP-Pi_job918_3d512_36A_sharpened.mrc (#6.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99925791 0.00048003 -0.03851493 6.37580270  
0.00057693 0.99962364 0.02742699 -4.82307494  
0.03851360 -0.02742886 0.99888155 -1.00344852  
Axis -0.58008527 -0.81455511 0.00102469  
Axis point 30.95074567 -0.00000000 168.39562229  
Rotation angle (degrees) 2.71010244  
Shift along axis 0.22912285  
  

> mmaker #6.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with Pre2_GDP-
Pi_RSR-0-coot-6.pdb, chain A (#6.1), sequence alignment score = 11579.8  
RMSD between 2684 pruned atom pairs is 0.593 angstroms; (across all 2903
pairs: 3.693)  
  

> hide #!6 models

> show #!7 models

> volume #7.2 step 1

> volume #7.2 level 3

> mmaker #7.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with Pre2_GDP-
Pi-1_RSR-0-coot-3.pdb, chain A (#7.1), sequence alignment score = 11579.8  
RMSD between 2684 pruned atom pairs is 0.593 angstroms; (across all 2903
pairs: 3.694)  
  

> fitmap #7.2 inMap #19

Fit map pre2_GDP-Pi-1_job998_44A_sharpened.mrc in map 70S_AP_v2.cif-coot-2.pdb
map 3 using 462332 points  
correlation = 0.622, correlation about mean = 0.2877, overlap = 7.5e+05  
steps = 148, shift = 0.675, angle = 3.58 degrees  
  
Position of pre2_GDP-Pi-1_job998_44A_sharpened.mrc (#7.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99886286 -0.01210352 -0.04611391 9.85727100  
0.01395361 0.99910177 0.04001178 -9.12187525  
0.04558821 -0.04060973 0.99813454 0.02000062  
Axis -0.64573543 -0.73448519 0.20870376  
Axis point 10.04362423 0.00000000 218.25667659  
Rotation angle (degrees) 3.57908016  
Shift along axis 0.33886737  
  

> hide #!7 models

> show #!7 models

> hide #!7 models

> close #8.1#8.3-4

> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/sharpened/chimeric_GDP1_job1099_5A_sharpened.mrc

Opened chimeric_GDP1_job1099_5A_sharpened.mrc as #20, grid size 288,288,288,
pixel 1.16, shown at level 4.74, step 2, values float32  

> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb

Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.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  
x | No description available  
y | No description available  
z | No description available  
  

> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb

Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb #22  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> close #22

> hide #21 atoms

> show #21 cartoons

> volume #20 step 1

> volume #20 level 3

> ui mousemode right select

> ui mousemode right pivot

> volume #20 level 2.132

> fitmap #8.2 inMap #19

Fit map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc in map 70S_AP_v2.cif-
coot-2.pdb map 3 using 3407857 points  
correlation = 0.6627, correlation about mean = 0.455, overlap = 5.748e+06  
steps = 192, shift = 0.8, angle = 4.93 degrees  
  
Position of chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#8.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99674298 0.04064621 -0.06965142 5.34833182  
-0.03854989 0.99877003 0.03118220 1.09060991  
0.07083319 -0.02839558 0.99708392 -6.05418170  
Axis -0.34653792 -0.81713761 -0.46064910  
Axis point 88.18353800 0.00000000 72.88378808  
Rotation angle (degrees) 4.93131208  
Shift along axis 0.04427522  
  

> show #!8 models

> volume #8.2 level 3

> rename #20 id 8.3

> rename #21 id 8.1

> mmaker #8.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
Chimeric_GDP-1-sw1-v2-RSR-0-coot-4.pdb, chain A (#8.1), sequence alignment
score = 11574.9  
RMSD between 2758 pruned atom pairs is 0.493 angstroms; (across all 2903
pairs: 1.280)  
  

> fitmap #8.3 inMap #19

Fit map chimeric_GDP1_job1099_5A_sharpened.mrc in map 70S_AP_v2.cif-coot-2.pdb
map 3 using 910340 points  
correlation = 0.5981, correlation about mean = 0.3543, overlap = 1.107e+06  
steps = 120, shift = 0.791, angle = 4.94 degrees  
  
Position of chimeric_GDP1_job1099_5A_sharpened.mrc (#8.3) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99673727 0.04088535 -0.06959311 5.28011210  
-0.03877132 0.99875269 0.03146197 1.10290130  
0.07079264 -0.02866110 0.99707921 -5.99422918  
Axis -0.34905673 -0.81503820 -0.46246310  
Axis point 87.44355332 0.00000000 71.92277294  
Rotation angle (degrees) 4.94055836  
Shift along axis 0.03014444  
  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!9 models

> close #9.2

> mmaker #9.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
Chimeric_GDP-2-RSR-0-coot-2.pdb, chain A (#9.1), sequence alignment score =
11574.9  
RMSD between 2736 pruned atom pairs is 0.476 angstroms; (across all 2903
pairs: 2.675)  
  

> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP2/sharpened/chimeric_GDP2_job914_5A_sharpened_b100.mrc

Opened chimeric_GDP2_job914_5A_sharpened_b100.mrc as #20, grid size
288,288,288, pixel 1.16, shown at level 3.42, step 2, values float32  

> rename #20 id 9.2

> volume #9.2 step 1

> volume #9.2 level 3

> fitmap #9.2 inMap #19

Fit map chimeric_GDP2_job914_5A_sharpened_b100.mrc in map 70S_AP_v2.cif-
coot-2.pdb map 3 using 370530 points  
correlation = 0.6538, correlation about mean = 0.1891, overlap = 5.64e+05  
steps = 84, shift = 0.317, angle = 2.25 degrees  
  
Position of chimeric_GDP2_job914_5A_sharpened_b100.mrc (#9.2) relative to
70S_AP_v2.cif-coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99947455 -0.00860105 -0.03125146 6.65433231  
0.00929534 0.99971169 0.02213910 -5.32206985  
0.03105203 -0.02241796 0.99926633 -1.03892385  
Axis -0.56645399 -0.79206438 0.22751682  
Axis point 40.09853146 0.00000000 216.05498401  
Rotation angle (degrees) 2.25401394  
Shift along axis 0.20967622  
  

> volume #9.2 level 2.645

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11.1 atoms

> show #!11.1 cartoons

> volume #11.2 step 1

> volume #11.2 level 3.672

> volume #11.2 level 3

> fitmap #11.2 inMap #19

Fit map h1_j620_3d288_44A_sharpened.mrc in map 70S_AP_v2.cif-coot-2.pdb map 3
using 452523 points  
correlation = 0.634, correlation about mean = 0.3063, overlap = 7.699e+05  
steps = 128, shift = 0.406, angle = 2.46 degrees  
  
Position of h1_j620_3d288_44A_sharpened.mrc (#11.2) relative to 70S_AP_v2.cif-
coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99931738 -0.01108434 -0.03524070 7.64812597  
0.01185008 0.99969657 0.02159480 -5.55226982  
0.03499064 -0.02199766 0.99914551 -1.65032654  
Axis -0.50817103 -0.81870887 0.26735369  
Axis point 54.18079252 0.00000000 219.11824958  
Rotation angle (degrees) 2.45825718  
Shift along axis 0.21791560  
  

> mmaker #11.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
70S_tRNA_c1_real_space_refined.pdb, chain A (#11.1), sequence alignment score
= 11577  
RMSD between 2606 pruned atom pairs is 0.808 angstroms; (across all 2903
pairs: 3.806)  
  

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!11 models

> volume #12.2 step 1

> volume #12.2 level 3

> mmaker #12.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
70S_tRNA_c2_real_space_refined.pdb, chain A (#12.1), sequence alignment score
= 11577  
RMSD between 2521 pruned atom pairs is 1.061 angstroms; (across all 2903
pairs: 3.858)  
  

> close #12.1

> close #11.1

> rename #13 id 11.1

> rename #14 id 12.1

> mmaker #11.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
70S_tRNA_c1_RSR-1-coot-4.pdb, chain A (#11.1), sequence alignment score =
11577  
RMSD between 2606 pruned atom pairs is 0.808 angstroms; (across all 2903
pairs: 3.806)  
  

> mmaker #12.1/A to #10.1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 70S_AP_v2.cif-coot-2.pdb, chain A (#10.1) with
70S_tRNA_c2_RSR-1-coot-2.pdb, chain A (#12.1), sequence alignment score =
11577  
RMSD between 2521 pruned atom pairs is 1.061 angstroms; (across all 2903
pairs: 3.858)  
  

> show #!11.1 models

> hide #!11 models

> show #!11 models

> hide #!11.1 atoms

> show #!11.1 cartoons

> hide #!11 models

> show #!12.1 models

> hide #!12.1 atoms

> show #!12.1 cartoons

> fitmap #12.2 inMap #19

Fit map h2_j621_3d288_95A_sharpened.mrc in map 70S_AP_v2.cif-coot-2.pdb map 3
using 586949 points  
correlation = 0.5618, correlation about mean = 0.1438, overlap = 6.683e+05  
steps = 96, shift = 0.328, angle = 3.07 degrees  
  
Position of h2_j621_3d288_95A_sharpened.mrc (#12.2) relative to 70S_AP_v2.cif-
coot-2.pdb map 3 (#19) coordinates:  
Matrix rotation and translation  
0.99906561 -0.01574383 -0.04024966 9.52157163  
0.01701398 0.99936172 0.03141152 -8.13984605  
0.03972943 -0.03206698 0.99869579 -0.77880441  
Axis -0.59195940 -0.74583323 0.30547807  
Axis point 28.95354864 0.00000000 238.78317879  
Rotation angle (degrees) 3.07351752  
Shift along axis 0.19667617  
  

> hide #!12 models

> show #15 models

> hide #15 models

> show #16 models

> show #!17 models

> rename #19 23S_reference

> hide #!19 models

> save X:/Work/Projects/EF-G/g3/Final_Modelling/All_in_one.cxs includeMaps
> true

> hide #16 models

> hide #!17 models

> show #!8 models

> hide #!8.3 models

> select #1,8 /x :328

22 atoms, 22 bonds, 2 residues, 2 models selected  

> show sel & #8.1 atoms

> style sel & #8.1 stick

Changed 11 atom styles  

> volume #8.2 level 2.138

> hide #!8 models

> show #!1 models

> hide #!1.2 models

> show sel & #!1.1 atoms

> show #!1.2 models

> hide #!1 models

> show #16 models

> show #!17 models

> ui mousemode right select

> select #16/x:294

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

33 atoms, 32 bonds, 5 residues, 1 model selected  

> select up

5473 atoms, 5576 bonds, 704 residues, 1 model selected  

> color sel red

> select #17/x:294

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

33 atoms, 32 bonds, 5 residues, 1 model selected  

> select up

5480 atoms, 5581 bonds, 707 residues, 1 model selected  

> color sel orange

> select clear

> show #!18 models

> select #18/x:250

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

126 atoms, 125 bonds, 16 residues, 1 model selected  

> select up

4325 atoms, 4399 bonds, 555 residues, 1 model selected  

> color sel darkorange

> select clear

> select #17/x:246

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

126 atoms, 125 bonds, 16 residues, 1 model selected  

> select up

5480 atoms, 5581 bonds, 707 residues, 1 model selected  

> color sel yellow

> select clear

> hide #!18 models

> select #17/w:47

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

1631 atoms, 1820 bonds, 76 residues, 1 model selected  

> color sel blue

> color sel lightblue

> ui mousemode right pivot

> ui mousemode right select

> select #16/w:36

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

1631 atoms, 1821 bonds, 76 residues, 1 model selected  

> color sel blue

> color sel fadeblue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel dodgerblue

> select clear

> select #17/x:536

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

60 atoms, 61 bonds, 7 residues, 1 model selected  

> select up

5480 atoms, 5581 bonds, 707 residues, 1 model selected  

> color sel lightcoral

> select clear

> color sel mistyrose

> select #17/x:445

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

58 atoms, 60 bonds, 6 residues, 1 model selected  

> select up

5480 atoms, 5581 bonds, 707 residues, 1 model selected  

> color sel mistyrose

> color sel pink

> select clear

> ui mousemode right pivot

> select #16/x:353

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #16-17/x:37,328,354,356,358,361

118 atoms, 110 bonds, 12 residues, 2 models selected  

> style sel ball

Changed 118 atom styles  

> show sel atoms

> hide sel atoms

> select #16-17/x:37,328,353,356,358,361

126 atoms, 118 bonds, 12 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select #16-17/x:37,328,356,358,361

108 atoms, 102 bonds, 10 residues, 2 models selected  

> show sel atoms

> style sel sphere

Changed 108 atom styles  

> color sel byhetero

> style sel stick

Changed 108 atom styles  

> style sel ball

Changed 108 atom styles  

> show #!8 models

> hide #16 models

> hide #!17 models

> hide #!8.2 models

> show #!8.2 models

> hide #!8.2 models

> ui mousemode right select

> select #8.1/x:356

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 11 atom styles  

> show #!8.2 models

> volume #8.2 level 1.8

> volume #8.2 level 1.2

> volume #8.2 level 2

> hide #!8 models

> show #15 models

> show #16 models

> show #!17 models

> hide #15 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!6 models

> hide #!6 models

> select #17/x

5480 atoms, 5581 bonds, 8 pseudobonds, 707 residues, 3 models selected  
Alignment identifier is 17/x  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 361, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1270, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 296, in run  
f(shortcut_atoms(s))  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 933, in show_sequence  
run(session, 'sequence chain %s' % seq_chain_spec, log = False)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 140, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 232, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 128, in __init__  
self._set_residue_attributes()  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 721, in _set_residue_attributes  
self.session.change_tracker.add_modified(assigned, attr_name + " changed")  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified  
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,  
AttributeError: 'set' object has no attribute '_c_pointer'  
  
AttributeError: 'set' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified  
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,  
  
See log for complete Python traceback.  
  
Alignment identifier is 17/x  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 361, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1270, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 296, in run  
f(shortcut_atoms(s))  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 933, in show_sequence  
run(session, 'sequence chain %s' % seq_chain_spec, log = False)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 140, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 232, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 128, in __init__  
self._set_residue_attributes()  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 721, in _set_residue_attributes  
self.session.change_tracker.add_modified(assigned, attr_name + " changed")  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified  
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,  
AttributeError: 'set' object has no attribute '_c_pointer'  
  
AttributeError: 'set' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified  
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 457.30
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 19041)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: uk-UA
Locale: ('uk_UA', 'cp1251')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.11.8
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.3
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202011140750
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.2.2
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.4
    pywin32: 228
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.35.1
    WMI: 1.5.1

[Eric Pettersen]

Hi Valentyn,

Thanks for reporting this problem. Due to an oversight, some code didn't get committed and this problem was the result. I have committed the code just now and the fix will be in tomorrow's build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab