The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_20230509.cxs"
Opened cryosparc_P64_J385_006_volume_map.mrc as #4.1, grid size 520,520,520,
pixel 0.834, shown at level 0.15, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #4.2, grid size 520,520,520,
pixel 0.834, shown at level 0.15, step 1, values float32
Opened cryosparc_P64_J389_005_volume_map.mrc as #4.3, grid size 520,520,520,
pixel 0.834, shown at level 0.15, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #5, grid size 520,520,520,
pixel 0.834, shown at level 0.17, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #6, grid size 520,520,520,
pixel 0.834, shown at level 0.16, step 1, values float32
Log from Tue May 9 11:56:23 2023UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_20230508.cxs"
Opened cryosparc_P64_J385_006_volume_map.mrc as #4.1, grid size 520,520,520,
pixel 0.834, shown at level 0.19, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #4.2, grid size 520,520,520,
pixel 0.834, shown at level 0.19, step 1, values float32
Opened cryosparc_P64_J389_005_volume_map.mrc as #4.3, grid size 520,520,520,
pixel 0.834, shown at level 0.19, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #5, grid size 520,520,520,
pixel 0.834, shown at level 0.19, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #6, grid size 520,520,520,
pixel 0.834, shown at level 0.19, step 1, values float32
Log from Mon May 8 17:59:38 2023UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_I,II,II.cxs"
Opened cryosparc_P64_J385_006_volume_map.mrc as #4.1, grid size 520,520,520,
pixel 0.834, shown at level 0.199, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #4.2, grid size 520,520,520,
pixel 0.834, shown at level 0.199, step 1, values float32
Opened cryosparc_P64_J389_005_volume_map.mrc as #4.3, grid size 520,520,520,
pixel 0.834, shown at level 0.199, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #5, grid size 520,520,520,
pixel 0.834, shown at level 0.236, step 1, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #6, grid size 520,520,520,
pixel 0.834, shown at level 0.199, step 1, values float32
Log from Wed May 3 15:34:58 2023UCSF ChimeraX version: 1.2.4 (2021-05-14)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "G:/E167K man prep Au 2023/models structure I,II,III/J385-coot-13.pdb"
> "G:/E167K man prep Au 2023/models structure I,II,III/J387-coot-13.pdb"
> "G:/E167K man prep Au 2023/models structure I,II,III/J389-coot-13.pdb"
Summary of feedback from opening G:/E167K man prep Au 2023/models structure
I,II,III/J385-coot-13.pdb
---
warnings | Start residue of secondary structure not found: HELIX 177 177 LEU H
3 ALA H 22 1 20
Start residue of secondary structure not found: HELIX 178 178 VAL H 33 ALA H
48 1 16
Start residue of secondary structure not found: HELIX 179 179 ARG H 62 GLU H
70 1 9
Start residue of secondary structure not found: HELIX 180 180 LYS H 73 PRO H
79 1 7
Start residue of secondary structure not found: HELIX 181 181 ARG H 94 PHE H
106 1 13
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue SPD (6210 )
Summary of feedback from opening G:/E167K man prep Au 2023/models structure
I,II,III/J387-coot-13.pdb
---
warnings | Start residue of secondary structure not found: HELIX 177 177 LEU H
3 ALA H 22 1 20
Start residue of secondary structure not found: HELIX 178 178 VAL H 33 ALA H
48 1 16
Start residue of secondary structure not found: HELIX 179 179 ARG H 62 GLU H
70 1 9
Start residue of secondary structure not found: HELIX 180 180 LYS H 73 PRO H
79 1 7
Start residue of secondary structure not found: HELIX 181 181 ARG H 94 PHE H
106 1 13
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue SPD (6210 )
Summary of feedback from opening G:/E167K man prep Au 2023/models structure
I,II,III/J389-coot-13.pdb
---
warnings | Start residue of secondary structure not found: HELIX 177 177 LEU H
3 ALA H 22 1 20
Start residue of secondary structure not found: HELIX 178 178 VAL H 33 ALA H
48 1 16
Start residue of secondary structure not found: HELIX 179 179 ARG H 62 GLU H
70 1 9
Start residue of secondary structure not found: HELIX 180 180 LYS H 73 PRO H
79 1 7
Start residue of secondary structure not found: HELIX 181 181 ARG H 94 PHE H
106 1 13
7 messages similar to the above omitted
Cannot find LINK/SSBOND residue SPD (6210 )
Chain information for J385-coot-13.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | 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
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
Chain information for J387-coot-13.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | 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
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
Chain information for J389-coot-13.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | 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
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 cartoons
> hide atoms
> set bgColor white
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel light blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel silver
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel silver
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel yellow
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel green
executed J385_color_structure8 final.cxc
> select #1/6#2/6#3/6
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> color sel magenta
> select #1/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel orange
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> color sel magenta
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel cyan
> select clear
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel red
> color sel byhetero
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel cyan
> select #1/5#2/5#3/5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel lime
> color sel forest green
> color sel light sea green
> color sel forest green
> ui tool show "Color Actions"
> color sel saddle brown
> color sel green
> color sel saddle brown
> color sel green
> color sel purple
> ui tool show "Color Actions"
> color sel brown
> select #1/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> select #1/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel orange
> select #1/4#2/4#3/4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel forest green
> select clear
> ui tool show "Color Actions"
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel cornflower blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel tan
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> ui tool show "Color Actions"
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel powder blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel beige
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> lighting soft
> lighting soft
> lighting full
> lighting soft
> lighting soft
> lighting soft
> lighting full
> lighting simple
> lighting soft
> set bgColor black
> lighting simple
> set bgColor white
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel light steel blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel beige
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel dark grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> lighting simple
> lighting simple
> lighting soft
> lighting soft
> lighting simple
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel medium blue
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> color #3 cornflower blue
> undo
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> show #!2 models
> hide #!3 models
> color sel cornflower blue
> color sel blue
> color sel medium blue
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color #2 magenta
> undo
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3
148561 atoms, 160717 bonds, 11 pseudobonds, 11260 residues, 3 models selected
> ~select #3
Nothing selected
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel magenta
> show #!2 models
> show #!1 models
> view matrix camera
> 0.73431,0.034642,0.67793,855.67,-0.67652,-0.04483,0.73506,901.28,0.055856,-0.99839,-0.0094836,228.98
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting soft
> lighting full
> lighting soft
> select clear
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> open "G:/E167K man prep Au 2023/J385 to
> J90/maps/cryosparc_P64_J385_006_volume_map.mrc" "G:/E167K man prep Au
> 2023/J385 to J90/maps/cryosparc_P64_J387_005_volume_map.mrc" "G:/E167K man
> prep Au 2023/J385 to J90/maps/cryosparc_P64_J389_005_volume_map.mrc"
Opened cryosparc_P64_J385_006_volume_map.mrc as #4.1, grid size 520,520,520,
pixel 0.834, shown at level 0.235, step 4, values float32
Opened cryosparc_P64_J387_005_volume_map.mrc as #4.2, grid size 520,520,520,
pixel 0.834, shown at level 0.236, step 4, values float32
Opened cryosparc_P64_J389_005_volume_map.mrc as #4.3, grid size 520,520,520,
pixel 0.834, shown at level 0.235, step 4, values float32
> volume #4 step 1
> select #1,2,3/6
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> volume zone #4 nearAtoms sel & #1,2,3 range 5
> select #1,2,3/6
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> select ~sel
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 16 models selected
> hide sel cartoons
> volume #4 level 0,19
Surface level must be a single value
> volume #4 level 0.19
> volume #4.1 level 0.1348
> hide #!3 models
> hide #!2 models
> hide #!1 models
> volume #4.1 level 0.15
> volume #4.2 level 0.15
> volume #4.1 style mesh
> volume #4.2 style mesh
> volume #4.3 style mesh
> show #!1 models
> show #!2 models
> show #!3 models
> select clear
> volume #4.2 color #0077ff
> volume #4.2 color #4400ff
> volume #4.2 color blue
> volume #4.2 color #1818ff
> volume #4.2 color #1616ff
> volume #4.2 color blue
> volume #4.2 color #0000cc
> volume #4.2 color blue
> volume #4.2 color blue
> volume #4 level 0.19
> volume #4 level 0.21
> volume #4 level 0.199
> volume #4 level 0.19
> volume #4 level 0.19 style surface
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> volume #4 level 0.18 style surface
> volume #4 level 0.199 style surface
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> camera position
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> view matrix
camera position:
0.97349,-0.036094,-0.22587,165.67,0.19599,-0.3775,0.90503,558.22,-0.11793,-0.9253,-0.36042,108.23
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.2,1,0,0,0,0,1,0,0,0,0,1,0,#4.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.3,1,0,0,0,0,1,0,0,0,0,1,0,#4.3.1,1,0,0,0,0,1,0,0,0,0,1,0
> Window size 500500
Unknown command: Window size 500500
> windowsize 500 500
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2S.png" width 3500 height 3500 supersample 4 transparentBackground true
> hide #!1 models
> hide #!2 models
> hide #!3 models
> select #1
148570 atoms, 160717 bonds, 11 pseudobonds, 11269 residues, 3 models selected
> select #2
148567 atoms, 160717 bonds, 11 pseudobonds, 11266 residues, 3 models selected
> select #3
148561 atoms, 160717 bonds, 11 pseudobonds, 11260 residues, 3 models selected
> select #1
148570 atoms, 160717 bonds, 11 pseudobonds, 11269 residues, 3 models selected
> show #!1 models
> select #2
148567 atoms, 160717 bonds, 11 pseudobonds, 11266 residues, 3 models selected
> ~select #2
Nothing selected
> cartoon #1,4
> select #1.2.3/5,6,4
Nothing selected
> show #!2 models
> show #!3 models
> hide #!4 models
> select #1,2,3/5,6,4
15130 atoms, 16014 bonds, 1399 residues, 3 models selected
> volume zone #5 nearAtoms sel & #1,2,3 range 5
> volume zone #4 nearAtoms sel & #1,2,3 range 5
> show #!4 models
> select #1,2,3/6
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> volume zone #4 nearAtoms sel & #1,2,3 range 5
> volume zone #4 nearAtoms sel & #1,2,3 range 2,5
Invalid "range" argument: Expected a number
> volume zone #4 nearAtoms sel & #1,2,3 range 2.5
> select ~sel
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 16 models selected
> hide sel cartoons
> volume zone #4 nearAtoms sel & #1,2,3 range 1
> undo
> volume zone #4 nearAtoms sel & #1,2,3 range 2
> volume zone #4 nearAtoms sel & #1,2,3 range 3
> select ~sel
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> hide #!4 models
> view camera matrix
> 0.73431,0.034642,0.67793,855.67,-0.67652,-0.04483,0.73506,901.28,0.055856,-0.99839,-0.0094836,228.98
Expected an objects specifier or a view name or a keyword
> view camera matrix:
> 0.73431,0.034642,0.67793,855.67,-0.67652,-0.04483,0.73506,901.28,0.055856,-0.99839,-0.0094836,228.98
Expected an objects specifier or a view name or a keyword
> camera matrix:
> 0.73431,0.034642,0.67793,855.67,-0.67652,-0.04483,0.73506,901.28,0.055856,-0.99839,-0.0094836,228.98
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> lighting soft
> lighting simple
> open "G:/E167K man prep Au 2023/J385 to
> J90/maps/cryosparc_P64_J387_005_volume_map.mrc"
Opened cryosparc_P64_J387_005_volume_map.mrc as #5, grid size 520,520,520,
pixel 0.834, shown at level 0.236, step 4, values float32
> open "G:/E167K man prep Au 2023/J385 to
> J90/maps/cryosparc_P64_J387_005_volume_map.mrc"
Opened cryosparc_P64_J387_005_volume_map.mrc as #6, grid size 520,520,520,
pixel 0.834, shown at level 0.236, step 4, values float32
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> volume zone #4 nearAtoms sel & #1,2,3 range 3
> show #!4 models
> select #2/5
1625 atoms, 1813 bonds, 78 residues, 1 model selected
> select #2
148567 atoms, 160717 bonds, 11 pseudobonds, 11266 residues, 3 models selected
> ~select #2
Nothing selected
> select #2
148567 atoms, 160717 bonds, 11 pseudobonds, 11266 residues, 3 models selected
> select #2/5
1625 atoms, 1813 bonds, 78 residues, 1 model selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> lighting soft
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> select #1
148570 atoms, 160717 bonds, 11 pseudobonds, 11269 residues, 3 models selected
> ~select #1
Nothing selected
> select #1,2,3/5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> select #1,2,3/6
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> select ~sel
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 20 models selected
> hide sel cartoons
> volume zone #4 nearAtoms sel & #1,2,3 range 2.5
> volume zone #4 nearAtoms sel & #1,2,3 range 2.5
> select #1,2,3/6
8566 atoms, 8685 bonds, 1084 residues, 3 models selected
> volume zone #4 nearAtoms sel & #1,2,3 range 2.5
> view matrix camera:
> 0.97349,-0.036094,-0.22587,165.67,0.19599,-0.3775,0.90503,558.22,-0.11793,-0.9253,-0.36042,108.23
Expected a keyword
> view matrix camera
> 0.97349,-0.036094,-0.22587,165.67,0.19599,-0.3775,0.90503,558.22,-0.11793,-0.9253,-0.36042,108.23
> windowsize 500 500
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2S_1.png" width 3500 height 3500 supersample 4 transparentBackground true
> select ~sel
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 20 models selected
> show sel cartoons
> hide #!1 models
> hide #!3 models
> ~select #6
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 18 models selected
> ~select #5
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 16 models selected
> ~select #4.3
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 14 models selected
> ~select #4.2
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 12 models selected
> ~select #4.1
437132 atoms, 473466 bonds, 33 pseudobonds, 32711 residues, 10 models selected
> select #4
7 models selected
> select #3
148561 atoms, 160717 bonds, 11 pseudobonds, 11260 residues, 3 models selected
> view matrix camera
> 0.73431,0.034642,0.67793,855.67,-0.67652,-0.04483,0.73506,901.28,0.055856,-0.99839,-0.0094836,228.98
> lighting soft
> select #1,2,3/5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> volume zone #5 nearAtoms sel & #1,2,3 range 2.5
> volume zone #5 nearAtoms sel & #1,2,3 range 2.5
> volume zone #5 nearAtoms sel & #1,2,3 range 2.5
> show #!5 models
> volume #5 step 1
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #6 color #005d00
> volume #6 step 1
> volume #6 level 0.199
> select #1,2,3/4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> volume zone #6 nearAtoms sel & #1,2,3 range 2.5
> show #!6 models
> hide #!6 models
> show #!6 models
> select #1/4#2/4#3/4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color (#!2 & sel) yellow
> lighting soft
> hide #!4.1 models
> hide #!4.3 models
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view matrix camera
> 0.73431,0.034642,0.67793,855.67,-0.67652,-0.04483,0.73506,901.28,0.055856,-0.99839,-0.0094836,228.98
> lighting simple
> view matrix
camera position:
0.74688,0.085806,0.6594,837.2,-0.65158,-0.10357,0.75148,918.07,0.13278,-0.99091,-0.021443,217.86
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.2,1,0,0,0,0,1,0,0,0,0,1,0,#4.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.3,1,0,0,0,0,1,0,0,0,0,1,0,#4.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0
> windowsize 500 500
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S.png" width 3500 height 3500 supersample 4
> view matrix camera
> 0.74688,0.085806,0.6594,837.2,-0.65158,-0.10357,0.75148,918.07,0.13278,-0.99091,-0.021443,217.86
> show #!4.1 models
> hide #!4.2 models
> windowsize 500 500
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_I.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> show #!1 models
> hide #!2 models
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_I.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> show #!4.3 models
> hide #!4.1 models
> show #!3 models
> hide #!1 models
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_III.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> show #!4.2 models
> show #!2 models
> hide #!3 models
> hide #!4.3 models
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_II.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> lighting soft
> lighting full
> select #1/4#2/4#3/4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color (#!2 & sel) lime
> show #!1 models
> show #!3 models
> lighting simple
> hide #!2 models
> show #!4.1 models
> hide #!4.2 models
> hide #!3 models
> windowsize 500 500
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_I.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> show #!2 models
> hide #!1 models
> show #!4.2 models
> hide #!4.1 models
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_II.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> show #!3 models
> hide #!2 models
> show #!4.3 models
> hide #!4.2 models
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_III.png" width 3500 height 3500 supersample 4 transparentBackground
> true
> show #!2 models
> hide #!3 models
> show #!4.2 models
> hide #!4.3 models
> lighting full
> lighting soft
> lighting simple
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_I,II,II.cxs" includeMaps true
——— End of log from Wed May 3 15:34:58 2023 ———
opened ChimeraX session
> show #!1 models
> show #!3 models
> ui tool show "Color Actions"
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel steel blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel dark khaki
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel dark grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel steel blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel khaki
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel dark grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> ui tool show "Color Actions"
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel steel blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel wheat
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel dark grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> select clear
> select clear
> hide #!4.2 models
> hide #!5 models
> hide #!6 models
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel slate blue
> color sel medium blue
> color sel blue
> color sel light sea green
> show #!6 models
> ui tool show "Color Actions"
> color sel medium spring green
> color sel dark turquoise
> color sel medium spring green
> color sel olive drab
> color sel dark turquoise
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> show #!2 models
> hide #!3 models
> color sel hot pink
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> show #!3 models
> hide #!2 models
> ui tool show "Color Actions"
> color sel cyan
> color sel dark turquoise
> color sel medium spring green
> color sel dark turquoise
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!3 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> lighting simple
> lighting soft
> lighting full
> lighting simple
> view camera matrix
> 0.74688,0.085806,0.6594,837.2,-0.65158,-0.10357,0.75148,918.07,0.13278,-0.99091,-0.021443,217.86
Expected an objects specifier or a view name or a keyword
> view matrix camera
> 0.74688,0.085806,0.6594,837.2,-0.65158,-0.10357,0.75148,918.07,0.13278,-0.99091,-0.021443,217.86
> show #!2 models
> hide #!3 models
> hide #!4.1 models
> hide #!4.3 models
> select clear
> volume #5 level 0.199
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S.png" width 3500 height 3500 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_1.png" width 3500 height 3500 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_2.png" width 5000 height 5000 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_2.png" width 5000 height 5000 supersample 3
> transparentBackground true
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S.png" width 5000 height 5000 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_1.png" width 5000 height 5000 supersample 1
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_1.png" width 1000 height 1000 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S.png" width 1500 height 1500 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S.png" width 1500 height 1500 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_1.png" width 2500 height 2500 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S.png" width 2000 height 2000 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_2500/4x.png" width 2500 height 2500 supersample 4
> transparentBackground true
Directory "G:/E167K man prep Au 2023/structural figures E167K RF2
I,II,III/fresh figures/J387 70S_2500" does not exist
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_12500.png" width 2500 height 2500 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_2500.png" width 2500 height 2500 supersample 1
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387 70S_2500_1.png" width 2500 height 2500 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387.png" width 2500 height 2500 supersample 4
> transparentBackground true
> show #!1 models
> hide #!2 models
> show #!4.1 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> select #1/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel orange
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> ui tool show "Color Actions"
> color sel dark orange
> color sel dark orange
> show #!4.1 models
> volume #4.1 level 0.19
> volume #4.1 level 0.21
> volume #4.1 level 0.18
> volume #4.1 level 0.15
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> volume #4.1 level 0.19
> volume #5 level 0.19
> volume #4.2 level 0.19
> volume #4.3 level 0.19
> volume #6 level 0.19
> view matrix camera
> 0.74688,0.085806,0.6594,837.2,-0.65158,-0.10357,0.75148,918.07,0.13278,-0.99091,-0.021443,217.86
> select clear
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J385.png" width 2500 height 2500 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J385.png" width 2500 height 2500 supersample 4
> transparentBackground true
> show #!3 models
> hide #!1 models
> show #!4.3 models
> hide #!4.1 models
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J389.png" width 2500 height 2500 supersample 4
> transparentBackground true
> show #!2 models
> hide #!3 models
> show #!4.2 models
> hide #!4.3 models
> select #2/6
2856 atoms, 2895 bonds, 362 residues, 1 model selected
> color sel magenta
> select clear
> select clear
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 2500 height 2500 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_20230508.cxs" includeMaps true
——— End of log from Mon May 8 17:59:38 2023 ———
opened ChimeraX session
> hide #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> show #!3 models
> hide #!2 models
> ui tool show "Color Actions"
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel cadet blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel wheat
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel dark grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel dodger blue
> color sel cornflower blue
> color sel royal blue
> select clear
> select #3/6
2855 atoms, 2895 bonds, 361 residues, 1 model selected
> color sel cornflower blue
> select clear
> volume #4.3 level 0.15
> volume #4.3 level 0.19
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J389_1.png" width 2500 height 2500 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J389_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> ui tool show "Color Actions"
> open "G:/E167K man prep Au 2023/J385_color_structure8 final.cxc"
> select /1
188236 atoms, 209646 bonds, 3 pseudobonds, 9691 residues, 6 models selected
> color sel silver
> select /2
99394 atoms, 110814 bonds, 3 pseudobonds, 5020 residues, 6 models selected
> color sel light blue
> select /g|/h|/i|/j|/k|/l|/m|/n|/o|/p|/q|/r|/s|/t|/u|/v|/w|/x|/y|/z
57105 atoms, 57936 bonds, 7245 residues, 3 models selected
> color sel cadet blue
> select
> /B|/C|/D|/E|/F|/G|/H|/I|/J|/K|/L|/M|/N|/O|/P|/Q|/R|/S|/T|/U|/V|/W|/X|/Y|/Z|/a|/b|/c|/d|/e|/f
78171 atoms, 79191 bonds, 27 pseudobonds, 10068 residues, 9 models selected
> color sel wheat
> select /3
7661 atoms, 8550 bonds, 371 residues, 3 models selected
> color sel dim grey
> select /4
1689 atoms, 1890 bonds, 81 residues, 3 models selected
> color sel green
> select /5
4875 atoms, 5439 bonds, 234 residues, 3 models selected
> color sel brown
executed J385_color_structure8 final.cxc
> select clear
> volume #6 level 0.25
> volume #6 level 0.15
> hide #!5 models
> hide #!4.3 models
> hide #!4 models
> hide #!3 models
> volume #6 level 0.17
> volume #6 level 0.19
> volume #6 level 0.12
> volume #6 level 0.13
> volume #6 level 0.14
> volume #6 level 0.15
> volume #6 level 0.16
> volume #6 level 0.17
> volume #6 level 0.18
> volume #6 level 0.16
> show #!5 models
> hide #!6 models
> volume #5 level 0.12
> volume #5 level 0.14
> volume #5 level 0.15
> volume #5 level 0.16
> volume #5 level 0.19
> volume #5 level 0.199
> volume #5 level 0.21
> volume #5 level 0.18
> volume #5 level 0.16
> volume #5 level 0.165
> volume #5 level 0.17
> show #!6 models
> show #!4.3 models
> volume #4.3 level 0.12
> volume #4.3 level 0.14
> volume #4.3 level 0.15
> volume #4.3 level 0.16
> volume #4.3 level 0.19
> volume #4.3 level 0.15
> show #!3 models
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J389_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> show #!4.2 models
> hide #!3 models
> hide #!4.3 models
> volume #4.2 level 0.15
> volume #4.2 level 0.16
> volume #4.2 level 0.15
> show #!2 models
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> show #!4.3 models
> hide #!4.3 models
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 5000 height 5000 supersample 3
> transparentBackground true
> view matrix camera
> 0.74688,0.085806,0.6594,837.2,-0.65158,-0.10357,0.75148,918.07,0.13278,-0.99091,-0.021443,217.86
> hide #!4.2 models
> show #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> windowsize 500 500
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 6000 height 6000 supersample 4
> transparentBackground true
> windowsize 1000 100
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1183+0+23 (frame:
1595x1222-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+0+23 (frame: 1595x1100-8-8) margins: 8, 31, 8, 8
minimum size: 394x402 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=410,441
maxtrack=0,0)
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1183+8+31 (frame:
1595x1222+0+0) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+8+31 (frame: 1595x1100+0+0) margins: 8, 31, 8, 8
minimum size: 394x402 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=410,441
maxtrack=0,0)
> windowsize 800 800
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J387_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> show #!3 models
> hide #!2 models
> show #!4.3 models
> hide #!4.2 models
> windowsize 800 800
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J389_1.png" width 5000 height 5000 supersample 4
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J389_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> show #!4.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4.3 models
> volume #4.1 level 0.15
> volume #4.1 level 0.12
> volume #4.1 level 0.13
> volume #4.1 level 0.14
> volume #4.1 level 0.15
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> windowsize 800 800
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J385_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J385_1.png" width 5000 height 5000 supersample 3
> transparentBackground true
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/70S J385_1.png" width 5000 height 5000 supersample 4
> transparentBackground true
> hide #!1 models
> hide #!6 models
> hide #!5 models
> show #!4.2 models
> show #!4.3 models
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/E167K
> RF2_70S_20230509.cxs" includeMaps true
——— End of log from Tue May 9 11:56:23 2023 ———
opened ChimeraX session
> show #!5 models
> show #!6 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!4.2 models
> hide #!4.3 models
> lighting simple
> lighting soft
> lighting simple
> windowsize 500 500
> save "C:/Users/shrpu756/Desktop/structural figures E167K RF2
> I,II,III/J385_500*500.png" width 500 height 500 supersample 4
> transparentBackground true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.4\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 1.2.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\image_formats\save.py", line 123, in save_image
i.save(path, format_name, **metadata)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\PIL\Image.py",
line 2155, in save
fp = builtins.open(filename, "w+b")
OSError: [Errno 22] Invalid argument: 'C:/Users/shrpu756/Desktop/structural
figures E167K RF2 I,II,III/J385_500*500.png'
OSError: [Errno 22] Invalid argument: 'C:/Users/shrpu756/Desktop/structural
figures E167K RF2 I,II,III/J385_500*500.png'
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\PIL\Image.py",
line 2155, in save
fp = builtins.open(filename, "w+b")
See log for complete Python traceback.
> save "G:/E167K man prep Au 2023/structural figures E167K RF2 I,II,III/fresh
> figures/J387_500*500.png" width 500 height 500 supersample 4
> transparentBackground true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.4\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 1.2.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\image_formats\\__init__.py", line 45, in save
save_image(session, path, format_name, **kw)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-
packages\chimerax\image_formats\save.py", line 123, in save_image
i.save(path, format_name, **metadata)
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\PIL\Image.py",
line 2155, in save
fp = builtins.open(filename, "w+b")
OSError: [Errno 22] Invalid argument: 'G:/E167K man prep Au 2023/structural
figures E167K RF2 I,II,III/fresh figures/J387_500*500.png'
OSError: [Errno 22] Invalid argument: 'G:/E167K man prep Au 2023/structural
figures E167K RF2 I,II,III/fresh figures/J387_500*500.png'
File "C:\Program Files\ChimeraX 1.2.4\bin\lib\site-packages\PIL\Image.py",
line 2155, in save
fp = builtins.open(filename, "w+b")
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 26.20.100.7262
OpenGL renderer: Intel(R) HD Graphics 530
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteDesk 800 G2 SFF
OS: Microsoft Windows 10 Enterprise (Build 18363)
Memory: 8,464,547,840
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
OSLanguage: en-US
Locale: ('sv_SE', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.4
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.0
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Reported by Shreya Pundit with version 1.2.4