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Opened 15 months ago
Closed 15 months ago
#15757 closed defect (can't reproduce)
ArrayMemoryError saving molecular surface in session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.9.dev202407300242 (2024-07-30 02:42:35 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9.dev202407300242 (2024-07-30)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Yeast_project\40S_4B\40S_4B_FL_map.cxs" format session
Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
level 0.004, step 1, values float32
Log from Fri Jun 14 15:32:28 2024UCSF ChimeraX version: 1.8.dev202312120034
(2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
> Science\\\Yeast_project\\\40S_4B\\\40S_4B_FL.cxs"
Log from Thu Jun 13 18:54:25 2024UCSF ChimeraX version: 1.8.dev202312120034
(2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
> Science\\\Yeast_project\\\40S_4B\\\40S_4B_1-98_RRM_AF3.cxs"
Log from Thu Jun 13 16:35:32 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Jose_TH_43S_PIC\New_RSR_models\PIN_5_real_space_refined.pdb" format
> pdb
Chain information for PIN_5_real_space_refined.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> ui tool show "Show Sequence Viewer"
> sequence chain /2
Alignment identifier is 1/2
> select /2:1150
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /2:1150-1157
175 atoms, 196 bonds, 8 residues, 1 model selected
> select /2:1150
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /2:1150-1626
10173 atoms, 11370 bonds, 477 residues, 1 model selected
> select ~sel & ##selected
94063 atoms, 98599 bonds, 9675 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select protein
Nothing selected
> show cartoons
> hide atoms
> set bgColor white
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/fold_40s_rrna_head_2024_06_12_22_44_model_0.cif"
Chain information for fold_40s_rrna_head_2024_06_12_22_44_model_0.cif #2
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_40s_rrna_head_2024_06_12_22_44_model_0.cif, chain A (#2), sequence
alignment score = 1887
RMSD between 441 pruned atom pairs is 0.742 angstroms; (across all 477 pairs:
1.140)
> select add #2
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> hide sel atoms
> select subtract #2
Nothing selected
> lighting soft
> graphics silhouettes true
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder/fold_2024_06_13_01_16_model_0.cif"
Chain information for fold_2024_06_13_01_16_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
> ui tool show Matchmaker
> matchmaker #3 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
1887
RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
1.036)
> matchmaker #3 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
1887
RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
1.036)
> select add #3
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> hide sel atoms
> select subtract #3
Nothing selected
> hide #2 models
> select add #1
10173 atoms, 11370 bonds, 477 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> surface sel
> hide sel atoms
> surface hidePatches (#!1 & sel)
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> select add #4
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select subtract #1
104236 atoms, 109969 bonds, 10152 residues, 2 models selected
> surface hidePatches sel
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #!4 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#4), sequence alignment score = 5525.6
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)
> select clear
> color #4 yellow
> select #1/2:1361
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10173 atoms, 11370 bonds, 477 residues, 2 models selected
> select clear
> select #1/2:1373
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10173 atoms, 11370 bonds, 477 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> select add #4/U:47
10180 atoms, 11376 bonds, 478 residues, 3 models selected
> select up
10332 atoms, 11529 bonds, 497 residues, 3 models selected
> select up
11018 atoms, 12227 bonds, 583 residues, 3 models selected
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select add #4/D:126
11025 atoms, 12233 bonds, 584 residues, 3 models selected
> select up
11150 atoms, 12360 bonds, 600 residues, 3 models selected
> select up
12792 atoms, 14027 bonds, 810 residues, 3 models selected
> select up
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select down
12792 atoms, 14027 bonds, 810 residues, 3 models selected
> show #3 models
> hide #3 models
> select add #4/K:16
12803 atoms, 14038 bonds, 811 residues, 3 models selected
> select up
12934 atoms, 14172 bonds, 826 residues, 3 models selected
> select up
13601 atoms, 14858 bonds, 906 residues, 3 models selected
> select up
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select down
13601 atoms, 14858 bonds, 906 residues, 3 models selected
> select add #4/2:1333
13621 atoms, 14879 bonds, 907 residues, 3 models selected
> select up
51413 atoms, 57141 bonds, 2686 residues, 3 models selected
> select ~sel & ##selected
62996 atoms, 64198 bonds, 7943 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> select clear
> show #3 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder
> (2)/fold_2024_06_13_14_34_model_0.cif"
Chain information for fold_2024_06_13_14_34_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> select #5/C:45@O
1 atom, 1 residue, 1 model selected
> select #5/C:45@O
1 atom, 1 residue, 1 model selected
> select clear
> select add #5
14573 atoms, 15847 bonds, 1035 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> color #5 #ff55ffff
> color #5 red
> ui tool show Matchmaker
> matchmaker #5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
1887
RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
1.027)
> matchmaker #5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
1887
RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
1.027)
> hide #3 models
> select #5/D:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
735 atoms, 749 bonds, 98 residues, 1 model selected
> color sel cyan
> color sel lime
> select clear
> select #5/D:56
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
735 atoms, 749 bonds, 98 residues, 1 model selected
> select ~sel
152248 atoms, 162895 bonds, 12980 residues, 5 models selected
> select subtract #1
142075 atoms, 151525 bonds, 12503 residues, 5 models selected
> select subtract #2
131912 atoms, 140165 bonds, 12026 residues, 3 models selected
> select subtract #3
118074 atoms, 125067 bonds, 11089 residues, 2 models selected
> color sel yellow
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_1-98_AF3.cxs"
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/RRM/fold_rrm_2024_06_13_15_51_model_0.cif"
Chain information for fold_rrm_2024_06_13_15_51_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> select add #6
14522 atoms, 15797 bonds, 1024 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> hide #5 models
> show #5 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_1-98_RRM_AF3.cxs"
\u2014\u2014\u2014 End of log from Thu Jun 13 16:35:32 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/fold_4b_fl_2024_06_13_16_47_model_0.cif"
Chain information for fold_4b_fl_2024_06_13_16_47_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> hide #!4 models
> show #!4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #7 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 1887
RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
1.026)
> matchmaker #7 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C (#7), sequence alignment
score = 3.14629e+230
Fewer than 3 residues aligned; cannot match PIN_5_real_space_refined.pdb,
chain 2 with fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C
> select clear
> show #5 models
> select #7/D:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
91 atoms, 93 bonds, 12 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> color sel red
> select clear
> hide #5 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> select #7/D:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> select ~sel & ##selected
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> color sel yellow
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
\u2014\u2014\u2014 End of log from Thu Jun 13 18:54:25 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/postprocess.mrc"
Opened postprocess.mrc as #8, grid size 360,360,360, pixel 1.2, shown at level
0.0128, step 2, values float32
> volume #8 level 0.005107
> volume #8 level 0.01186
> close #8
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/postprocess 1.mrc"
Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
level 0.0117, step 2, values float32
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select add #4
121498 atoms, 128561 bonds, 11525 residues, 2 models selected
> select subtract #4
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select add #4
121498 atoms, 128561 bonds, 11525 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,1,0,0,29.873,0,1,0,-26.112,0,0,1,-4.1724,#7,0.28189,0.89695,-0.3406,208.48,-0.59451,-0.11535,-0.79578,143.74,-0.75306,0.42681,0.50073,170.55
> view matrix models
> #4,0.82111,0.074806,0.56584,-60.523,0.37786,0.67177,-0.63714,95.401,-0.42778,0.73697,0.52334,8.5864,#7,-0.23912,0.96938,-0.055872,197.7,0.18694,-0.010503,-0.98231,165.67,-0.95282,-0.24534,-0.17871,148.8
> view matrix models
> #4,0.39428,0.28977,0.87211,-82.164,0.12554,0.92311,-0.36347,36.734,-0.91037,0.25279,0.32759,252.6,#7,-0.71788,0.69246,0.071801,189.85,-0.23969,-0.14901,-0.95935,152.45,-0.65361,-0.7059,0.27294,190.17
> view matrix models
> #4,0.93276,0.24233,0.26689,-61.721,-0.20029,0.96394,-0.17522,56.548,-0.29973,0.10998,0.94766,39.262,#7,-0.082117,0.92261,-0.3769,192.67,-0.49758,-0.36563,-0.7866,153.89,-0.86352,0.12294,0.48909,169.98
> view matrix models
> #4,0.90668,0.38695,-0.16792,-3.6645,-0.32198,0.89205,0.31713,0.28806,0.27251,-0.23347,0.9334,5.1958,#7,0.15199,0.69695,-0.70083,194.66,-0.85991,-0.25634,-0.44141,149.71,-0.48729,0.66974,0.56035,177.29
> view matrix models
> #4,0.83083,0.46289,-0.30895,22.476,-0.33038,0.85698,0.39553,-5.67,0.44785,-0.22655,0.86493,-18.087,#7,0.19167,0.55996,-0.80604,195.51,-0.90046,-0.22637,-0.37138,149.99,-0.39042,0.797,0.46084,174.54
> view matrix models
> #4,0.81586,0.41377,-0.40394,53.081,-0.43451,0.8996,0.043887,72.529,0.38154,0.13971,0.91373,-95.845,#7,0.28818,0.51166,-0.80942,198.5,-0.69035,-0.47477,-0.5459,155.39,-0.6636,0.7161,0.2164,155.68
> view matrix models
> #4,0.92225,0.36326,0.13231,-66.698,-0.33704,0.92311,-0.18513,90.197,-0.18939,0.12614,0.97377,7.703,#7,-0.055625,0.84179,-0.53694,182.84,-0.50438,-0.4878,-0.71249,154.45,-0.86169,0.23119,0.45172,165.44
> view matrix models
> #4,0.90839,0.41625,0.039549,-57.795,-0.40792,0.86146,0.30246,24.934,0.091829,-0.29088,0.95234,48.468,#7,-0.021182,0.78365,-0.62084,182.06,-0.8549,-0.33616,-0.39515,151.25,-0.51836,0.52239,0.67706,181.85
> view matrix models
> #4,0.84077,0.51864,-0.15529,-28.698,-0.44574,0.82595,0.34513,31.845,0.30726,-0.22096,0.92562,-4.1938,#7,0.04562,0.62803,-0.77685,182.43,-0.87659,-0.34777,-0.33263,152.83,-0.47907,0.69615,0.53466,174.88
> view matrix models
> #4,0.84077,0.51864,-0.15529,-50.435,-0.44574,0.82595,0.34513,42.879,0.30726,-0.22096,0.92562,-2.874,#7,0.04562,0.62803,-0.77685,160.69,-0.87659,-0.34777,-0.33263,163.86,-0.47907,0.69615,0.53466,176.2
> view matrix models
> #4,0.89894,0.43035,0.081855,-87.056,-0.41583,0.89706,-0.14958,114.17,-0.1378,0.10043,0.98536,2.6161,#7,-0.064087,0.79161,-0.60766,160.9,-0.53788,-0.54029,-0.64712,166.14,-0.84058,0.28538,0.46042,167.22
> view matrix models
> #4,0.82294,0.43483,0.36563,-128.34,-0.25543,0.85805,-0.44554,148.79,-0.50747,0.27326,0.8172,70.448,#7,-0.30188,0.84404,-0.44324,156.38,-0.2466,-0.51824,-0.81891,171.07,-0.9209,-0.13791,0.36459,169
> view matrix models
> #4,0.72434,0.68781,0.047535,-102.66,-0.68702,0.7143,0.13333,154.87,0.057748,-0.12923,0.98993,13.333,#7,-0.24052,0.59065,-0.77025,151.84,-0.71872,-0.64172,-0.26766,176.79,-0.65237,0.48922,0.57886,174.65
> view matrix models
> #4,0.72434,0.68781,0.047535,-93.022,-0.68702,0.7143,0.13333,168.08,0.057748,-0.12923,0.98993,9.714,#7,-0.24052,0.59065,-0.77025,161.48,-0.71872,-0.64172,-0.26766,190,-0.65237,0.48922,0.57886,171.04
> view matrix models
> #4,0.72434,0.68781,0.047535,-95.873,-0.68702,0.7143,0.13333,147.08,0.057748,-0.12923,0.98993,29.062,#7,-0.24052,0.59065,-0.77025,158.63,-0.71872,-0.64172,-0.26766,169,-0.65237,0.48922,0.57886,190.38
> view matrix models
> #4,0.85992,0.49465,-0.12597,-48.976,-0.47438,0.86556,0.16051,68.367,0.18843,-0.078265,0.97896,-5.6566,#7,0.043195,0.66049,-0.74959,166.62,-0.76918,-0.45683,-0.44685,158.7,-0.63758,0.59587,0.4883,185.75
> view matrix models
> #4,0.82107,0.52004,0.23539,-114.53,-0.48014,0.85219,-0.20793,141.5,-0.30873,0.057706,0.9494,68.51,#7,-0.25498,0.77694,-0.57563,161.58,-0.48539,-0.61771,-0.61873,164.17,-0.83629,0.12164,0.53462,189.05
> ui tool show "Fit in Map"
> fitmap #1 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
using 10173 atoms
average map value = 0.01768, steps = 280
shifted from previous position = 37.6
rotated from previous position = 39.4 degrees
atoms outside contour = 1813, contour level = 0.011685
Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.77406817 0.62549730 0.09783453 -108.84656169
-0.61873269 0.78014893 -0.09239861 173.02544428
-0.13412059 0.01098940 0.99090408 40.92544766
Axis 0.08141544 0.18265879 -0.97979962
Axis point 198.28970282 243.37991178 0.00000000
Rotation angle (degrees) 39.41561211
Shift along axis -17.35591133
> volume #8 level 0.008395
> volume #8 level 0.007367
> volume #8 level 0.006339
> volume #8 level 0.005928
> volume #8 level 0.0049
> volume #8 level 0.004694
> volume #8 level 0.004283
> volume #8 level 0.004077
> volume #8 level 0.003872
> volume #8 level 0.004077
> ui tool show "Hide Dust"
> surface dust #8 size 50.34
> view matrix models
> #4,0.82107,0.52004,0.23539,-116.39,-0.48014,0.85219,-0.20793,141.63,-0.30873,0.057706,0.9494,74.429,#7,-0.25498,0.77694,-0.57563,159.72,-0.48539,-0.61771,-0.61873,164.29,-0.83629,0.12164,0.53462,194.97
> view matrix models
> #4,0.78554,0.61095,0.098306,-102.93,-0.60821,0.79156,-0.059316,151.7,-0.11405,-0.013196,0.99339,42.954,#7,-0.21581,0.67608,-0.70451,158.32,-0.59736,-0.66215,-0.45245,167.16,-0.77239,0.32321,0.54677,193.9
> fitmap #1 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
using 10173 atoms
average map value = 0.01768, steps = 48
shifted from previous position = 0.0285
rotated from previous position = 0.0236 degrees
atoms outside contour = 97, contour level = 0.0040773
Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.77413240 0.62548017 0.09743502 -108.78348482
-0.61871031 0.78015823 -0.09246993 173.04062336
-0.13385284 0.01129992 0.99093679 40.84496958
Axis 0.08172445 0.18215188 -0.97986826
Axis point 198.35850392 243.27675668 0.00000000
Rotation angle (degrees) 39.41081833
Shift along axis -17.39328493
> fitmap #4 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
using 104236 atoms
average map value = 0.0104, steps = 108
shifted from previous position = 14.3
rotated from previous position = 5.98 degrees
atoms outside contour = 34631, contour level = 0.0040773
Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.81103895 0.56883502 0.13653773 -110.00386069
-0.55348062 0.82172712 -0.13573415 163.72215947
-0.18940709 0.03451469 0.98129186 49.38976006
Axis 0.14415361 0.27598498 -0.95029050
Axis point 220.17547445 262.06246433 0.00000000
Rotation angle (degrees) 36.19334027
Shift along axis -17.60721577
> fitmap #7 inMap #8
Fit molecule fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) to map postprocess
1.mrc (#8) using 17262 atoms
average map value = 0.01325, steps = 108
shifted from previous position = 13
rotated from previous position = 1.77 degrees
atoms outside contour = 2973, contour level = 0.0040773
Position of fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) relative to
postprocess 1.mrc (#8) coordinates:
Matrix rotation and translation
-0.22927120 0.66107322 -0.71443470 152.80411903
-0.57591627 -0.68385311 -0.44795691 178.76428159
-0.78470070 0.30875094 0.53751064 191.73888093
Axis 0.52122493 0.04839965 -0.85204580
Axis point 181.08241586 46.38734422 0.00000000
Rotation angle (degrees) 133.45675049
Shift along axis -75.07286549
> volume #8 style mesh
> hide #!4 models
> select subtract #4
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #8 style surface
> volume #8 step 1
> volume #8 level 0.0045
> volume #8 level 0.0035
> volume #8 style mesh
> show #!4 models
> volume #8 level 0.0045
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #4
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #4
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel orange
> select clear
> select add #4
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> view matrix models #4,1,0,0,-20.338,0,1,0,1.5317,0,0,1,-2.6363
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.73417,-0.011715,0.67887,-110.65,0.039726,0.99888,-0.025724,-0.60366,-0.67781,0.045854,0.73381,179.35
> view matrix models
> #4,0.9789,0.11074,-0.17176,-3.8946,-0.04979,0.94437,0.32509,-46.014,0.1982,-0.30968,0.92995,41.92
> view matrix models
> #4,0.017369,0.56222,-0.82681,227.8,0.33544,0.77573,0.53453,-130.18,0.9419,-0.28663,-0.17512,126.11
> view matrix models
> #4,-0.12811,0.98357,-0.12718,12.586,0.92087,0.07036,-0.38347,107.6,-0.36822,-0.16624,-0.91476,519.17
> view matrix models
> #4,0.5569,0.82779,0.068008,-131.09,0.01997,0.068512,-0.99745,419.38,-0.83034,0.55683,0.021623,248.94
> view matrix models
> #4,0.84123,0.44504,-0.30702,-21.878,-0.53641,0.61579,-0.57712,317.96,-0.067779,0.65018,0.75675,-81.698
> view matrix models
> #4,0.73797,0.6641,0.11988,-141.84,-0.62927,0.74137,-0.23323,234.59,-0.24376,0.096676,0.965,31.9
> view matrix models
> #4,0.73797,0.6641,0.11988,-108.61,-0.62927,0.74137,-0.23323,201.59,-0.24376,0.096676,0.965,35.063
> view matrix models
> #4,0.72535,0.63548,0.26463,-130.83,-0.54471,0.76491,-0.34381,203.26,-0.42091,0.10523,0.90098,82.196
> fitmap #4 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
using 104236 atoms
average map value = 0.0104, steps = 216
shifted from previous position = 20.7
rotated from previous position = 15.2 degrees
atoms outside contour = 38093, contour level = 0.0045
Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.81109770 0.56879176 0.13636883 -109.97657823
-0.55342535 0.82174938 -0.13582465 163.71638992
-0.18931694 0.03469710 0.98130281 49.31254596
Axis 0.14440007 0.27579500 -0.95030823
Axis point 220.19825708 262.01584691 0.00000000
Rotation angle (degrees) 36.18887777
Shift along axis -17.59058130
> select clear
> select #4/p:724
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
214 atoms, 217 bonds, 24 residues, 1 model selected
> select up
292 atoms, 298 bonds, 33 residues, 1 model selected
> select up
5114 atoms, 5246 bonds, 647 residues, 1 model selected
> select up
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> select up
184767 atoms, 198033 bonds, 15475 residues, 9 models selected
> select down
104236 atoms, 109969 bonds, 10152 residues, 2 models selected
> select down
5114 atoms, 5246 bonds, 647 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/r:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
2019 atoms, 2064 bonds, 258 residues, 1 model selected
> select up
2043 atoms, 2088 bonds, 261 residues, 1 model selected
> select up
2606 atoms, 2669 bonds, 330 residues, 1 model selected
> select up
99122 atoms, 104723 bonds, 9505 residues, 1 model selected
> select down
2606 atoms, 2669 bonds, 330 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/o:843
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
225 atoms, 224 bonds, 45 residues, 1 model selected
> select up
280 atoms, 279 bonds, 56 residues, 1 model selected
> select up
285 atoms, 283 bonds, 57 residues, 1 model selected
> select up
387 atoms, 385 bonds, 78 residues, 1 model selected
> select add #4/q:89
396 atoms, 393 bonds, 79 residues, 1 model selected
> select up
487 atoms, 486 bonds, 89 residues, 1 model selected
> select up
779 atoms, 784 bonds, 127 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/D:158
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> select ~sel & ##selected
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> volume #8 style surface
> volume #8
> volume #8 style mesh
> volume #8 style surface
> volume #8 level 0.004
> volume #8 style mesh
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_FL_map.cxs"
\u2014\u2014\u2014 End of log from Fri Jun 14 15:32:28 2024 \u2014\u2014\u2014
opened ChimeraX session
> close session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_AF_Fig5A.cxs"
Log from Fri Aug 9 17:46:46 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9.dev202407300242 (2024-07-30)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_AF-P34167-F1-model_v4.pdb"
4B_AF-P34167-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for eukaryotic translation initiation factor
4B (P34167) [more info...]
Chain information for 4B_AF-P34167-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | eukaryotic translation initiation factor 4B | IF4B_YEAST 1-436
> set bgColor white
> graphics silhouettes true
> lighting flat
> color magenta
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder/4B_AF_colored_5A.png" width 957
> height 585 supersample 3 transparentBackground true
> close session
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Yeast_project\40S_4B\4B_FL\Figure_session.cxs" format session
Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
level 0.004, step 1, values float32
Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
0.00408, step 2, values float32
Log from Fri Jul 5 12:41:39 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Yeast_project\40S_4B\40S_4B_FL_map.cxs" format session
Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
level 0.004, step 1, values float32
Log from Fri Jun 14 15:32:28 2024UCSF ChimeraX version: 1.8.dev202312120034
(2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
> Science\\\Yeast_project\\\40S_4B\\\40S_4B_FL.cxs"
Log from Thu Jun 13 18:54:25 2024UCSF ChimeraX version: 1.8.dev202312120034
(2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
> Science\\\Yeast_project\\\40S_4B\\\40S_4B_1-98_RRM_AF3.cxs"
Log from Thu Jun 13 16:35:32 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Jose_TH_43S_PIC\New_RSR_models\PIN_5_real_space_refined.pdb" format
> pdb
Chain information for PIN_5_real_space_refined.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> ui tool show "Show Sequence Viewer"
> sequence chain /2
Alignment identifier is 1/2
> select /2:1150
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /2:1150-1157
175 atoms, 196 bonds, 8 residues, 1 model selected
> select /2:1150
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /2:1150-1626
10173 atoms, 11370 bonds, 477 residues, 1 model selected
> select ~sel & ##selected
94063 atoms, 98599 bonds, 9675 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select protein
Nothing selected
> show cartoons
> hide atoms
> set bgColor white
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/fold_40s_rrna_head_2024_06_12_22_44_model_0.cif"
Chain information for fold_40s_rrna_head_2024_06_12_22_44_model_0.cif #2
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_40s_rrna_head_2024_06_12_22_44_model_0.cif, chain A (#2), sequence
alignment score = 1887
RMSD between 441 pruned atom pairs is 0.742 angstroms; (across all 477 pairs:
1.140)
> select add #2
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> hide sel atoms
> select subtract #2
Nothing selected
> lighting soft
> graphics silhouettes true
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder/fold_2024_06_13_01_16_model_0.cif"
Chain information for fold_2024_06_13_01_16_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
> ui tool show Matchmaker
> matchmaker #3 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
1887
RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
1.036)
> matchmaker #3 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
1887
RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
1.036)
> select add #3
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> hide sel atoms
> select subtract #3
Nothing selected
> hide #2 models
> select add #1
10173 atoms, 11370 bonds, 477 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> surface sel
> hide sel atoms
> surface hidePatches (#!1 & sel)
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> select add #4
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select subtract #1
104236 atoms, 109969 bonds, 10152 residues, 2 models selected
> surface hidePatches sel
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #!4 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#4), sequence alignment score = 5525.6
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)
> select clear
> color #4 yellow
> select #1/2:1361
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10173 atoms, 11370 bonds, 477 residues, 2 models selected
> select clear
> select #1/2:1373
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10173 atoms, 11370 bonds, 477 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> select add #4/U:47
10180 atoms, 11376 bonds, 478 residues, 3 models selected
> select up
10332 atoms, 11529 bonds, 497 residues, 3 models selected
> select up
11018 atoms, 12227 bonds, 583 residues, 3 models selected
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select add #4/D:126
11025 atoms, 12233 bonds, 584 residues, 3 models selected
> select up
11150 atoms, 12360 bonds, 600 residues, 3 models selected
> select up
12792 atoms, 14027 bonds, 810 residues, 3 models selected
> select up
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select down
12792 atoms, 14027 bonds, 810 residues, 3 models selected
> show #3 models
> hide #3 models
> select add #4/K:16
12803 atoms, 14038 bonds, 811 residues, 3 models selected
> select up
12934 atoms, 14172 bonds, 826 residues, 3 models selected
> select up
13601 atoms, 14858 bonds, 906 residues, 3 models selected
> select up
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select down
13601 atoms, 14858 bonds, 906 residues, 3 models selected
> select add #4/2:1333
13621 atoms, 14879 bonds, 907 residues, 3 models selected
> select up
51413 atoms, 57141 bonds, 2686 residues, 3 models selected
> select ~sel & ##selected
62996 atoms, 64198 bonds, 7943 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> select clear
> show #3 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder
> (2)/fold_2024_06_13_14_34_model_0.cif"
Chain information for fold_2024_06_13_14_34_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> select #5/C:45@O
1 atom, 1 residue, 1 model selected
> select #5/C:45@O
1 atom, 1 residue, 1 model selected
> select clear
> select add #5
14573 atoms, 15847 bonds, 1035 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> color #5 #ff55ffff
> color #5 red
> ui tool show Matchmaker
> matchmaker #5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
1887
RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
1.027)
> matchmaker #5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
1887
RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
1.027)
> hide #3 models
> select #5/D:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
735 atoms, 749 bonds, 98 residues, 1 model selected
> color sel cyan
> color sel lime
> select clear
> select #5/D:56
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
735 atoms, 749 bonds, 98 residues, 1 model selected
> select ~sel
152248 atoms, 162895 bonds, 12980 residues, 5 models selected
> select subtract #1
142075 atoms, 151525 bonds, 12503 residues, 5 models selected
> select subtract #2
131912 atoms, 140165 bonds, 12026 residues, 3 models selected
> select subtract #3
118074 atoms, 125067 bonds, 11089 residues, 2 models selected
> color sel yellow
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_1-98_AF3.cxs"
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/RRM/fold_rrm_2024_06_13_15_51_model_0.cif"
Chain information for fold_rrm_2024_06_13_15_51_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> select add #6
14522 atoms, 15797 bonds, 1024 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> hide #5 models
> show #5 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_1-98_RRM_AF3.cxs"
\u2014\u2014\u2014 End of log from Thu Jun 13 16:35:32 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/fold_4b_fl_2024_06_13_16_47_model_0.cif"
Chain information for fold_4b_fl_2024_06_13_16_47_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> hide #!4 models
> show #!4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #7 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 1887
RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
1.026)
> matchmaker #7 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C (#7), sequence alignment
score = 3.14629e+230
Fewer than 3 residues aligned; cannot match PIN_5_real_space_refined.pdb,
chain 2 with fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C
> select clear
> show #5 models
> select #7/D:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
91 atoms, 93 bonds, 12 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> color sel red
> select clear
> hide #5 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> select #7/D:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> select ~sel & ##selected
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> color sel yellow
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
\u2014\u2014\u2014 End of log from Thu Jun 13 18:54:25 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/postprocess.mrc"
Opened postprocess.mrc as #8, grid size 360,360,360, pixel 1.2, shown at level
0.0128, step 2, values float32
> volume #8 level 0.005107
> volume #8 level 0.01186
> close #8
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/postprocess 1.mrc"
Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
level 0.0117, step 2, values float32
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select add #4
121498 atoms, 128561 bonds, 11525 residues, 2 models selected
> select subtract #4
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select add #4
121498 atoms, 128561 bonds, 11525 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,1,0,0,29.873,0,1,0,-26.112,0,0,1,-4.1724,#7,0.28189,0.89695,-0.3406,208.48,-0.59451,-0.11535,-0.79578,143.74,-0.75306,0.42681,0.50073,170.55
> view matrix models
> #4,0.82111,0.074806,0.56584,-60.523,0.37786,0.67177,-0.63714,95.401,-0.42778,0.73697,0.52334,8.5864,#7,-0.23912,0.96938,-0.055872,197.7,0.18694,-0.010503,-0.98231,165.67,-0.95282,-0.24534,-0.17871,148.8
> view matrix models
> #4,0.39428,0.28977,0.87211,-82.164,0.12554,0.92311,-0.36347,36.734,-0.91037,0.25279,0.32759,252.6,#7,-0.71788,0.69246,0.071801,189.85,-0.23969,-0.14901,-0.95935,152.45,-0.65361,-0.7059,0.27294,190.17
> view matrix models
> #4,0.93276,0.24233,0.26689,-61.721,-0.20029,0.96394,-0.17522,56.548,-0.29973,0.10998,0.94766,39.262,#7,-0.082117,0.92261,-0.3769,192.67,-0.49758,-0.36563,-0.7866,153.89,-0.86352,0.12294,0.48909,169.98
> view matrix models
> #4,0.90668,0.38695,-0.16792,-3.6645,-0.32198,0.89205,0.31713,0.28806,0.27251,-0.23347,0.9334,5.1958,#7,0.15199,0.69695,-0.70083,194.66,-0.85991,-0.25634,-0.44141,149.71,-0.48729,0.66974,0.56035,177.29
> view matrix models
> #4,0.83083,0.46289,-0.30895,22.476,-0.33038,0.85698,0.39553,-5.67,0.44785,-0.22655,0.86493,-18.087,#7,0.19167,0.55996,-0.80604,195.51,-0.90046,-0.22637,-0.37138,149.99,-0.39042,0.797,0.46084,174.54
> view matrix models
> #4,0.81586,0.41377,-0.40394,53.081,-0.43451,0.8996,0.043887,72.529,0.38154,0.13971,0.91373,-95.845,#7,0.28818,0.51166,-0.80942,198.5,-0.69035,-0.47477,-0.5459,155.39,-0.6636,0.7161,0.2164,155.68
> view matrix models
> #4,0.92225,0.36326,0.13231,-66.698,-0.33704,0.92311,-0.18513,90.197,-0.18939,0.12614,0.97377,7.703,#7,-0.055625,0.84179,-0.53694,182.84,-0.50438,-0.4878,-0.71249,154.45,-0.86169,0.23119,0.45172,165.44
> view matrix models
> #4,0.90839,0.41625,0.039549,-57.795,-0.40792,0.86146,0.30246,24.934,0.091829,-0.29088,0.95234,48.468,#7,-0.021182,0.78365,-0.62084,182.06,-0.8549,-0.33616,-0.39515,151.25,-0.51836,0.52239,0.67706,181.85
> view matrix models
> #4,0.84077,0.51864,-0.15529,-28.698,-0.44574,0.82595,0.34513,31.845,0.30726,-0.22096,0.92562,-4.1938,#7,0.04562,0.62803,-0.77685,182.43,-0.87659,-0.34777,-0.33263,152.83,-0.47907,0.69615,0.53466,174.88
> view matrix models
> #4,0.84077,0.51864,-0.15529,-50.435,-0.44574,0.82595,0.34513,42.879,0.30726,-0.22096,0.92562,-2.874,#7,0.04562,0.62803,-0.77685,160.69,-0.87659,-0.34777,-0.33263,163.86,-0.47907,0.69615,0.53466,176.2
> view matrix models
> #4,0.89894,0.43035,0.081855,-87.056,-0.41583,0.89706,-0.14958,114.17,-0.1378,0.10043,0.98536,2.6161,#7,-0.064087,0.79161,-0.60766,160.9,-0.53788,-0.54029,-0.64712,166.14,-0.84058,0.28538,0.46042,167.22
> view matrix models
> #4,0.82294,0.43483,0.36563,-128.34,-0.25543,0.85805,-0.44554,148.79,-0.50747,0.27326,0.8172,70.448,#7,-0.30188,0.84404,-0.44324,156.38,-0.2466,-0.51824,-0.81891,171.07,-0.9209,-0.13791,0.36459,169
> view matrix models
> #4,0.72434,0.68781,0.047535,-102.66,-0.68702,0.7143,0.13333,154.87,0.057748,-0.12923,0.98993,13.333,#7,-0.24052,0.59065,-0.77025,151.84,-0.71872,-0.64172,-0.26766,176.79,-0.65237,0.48922,0.57886,174.65
> view matrix models
> #4,0.72434,0.68781,0.047535,-93.022,-0.68702,0.7143,0.13333,168.08,0.057748,-0.12923,0.98993,9.714,#7,-0.24052,0.59065,-0.77025,161.48,-0.71872,-0.64172,-0.26766,190,-0.65237,0.48922,0.57886,171.04
> view matrix models
> #4,0.72434,0.68781,0.047535,-95.873,-0.68702,0.7143,0.13333,147.08,0.057748,-0.12923,0.98993,29.062,#7,-0.24052,0.59065,-0.77025,158.63,-0.71872,-0.64172,-0.26766,169,-0.65237,0.48922,0.57886,190.38
> view matrix models
> #4,0.85992,0.49465,-0.12597,-48.976,-0.47438,0.86556,0.16051,68.367,0.18843,-0.078265,0.97896,-5.6566,#7,0.043195,0.66049,-0.74959,166.62,-0.76918,-0.45683,-0.44685,158.7,-0.63758,0.59587,0.4883,185.75
> view matrix models
> #4,0.82107,0.52004,0.23539,-114.53,-0.48014,0.85219,-0.20793,141.5,-0.30873,0.057706,0.9494,68.51,#7,-0.25498,0.77694,-0.57563,161.58,-0.48539,-0.61771,-0.61873,164.17,-0.83629,0.12164,0.53462,189.05
> ui tool show "Fit in Map"
> fitmap #1 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
using 10173 atoms
average map value = 0.01768, steps = 280
shifted from previous position = 37.6
rotated from previous position = 39.4 degrees
atoms outside contour = 1813, contour level = 0.011685
Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.77406817 0.62549730 0.09783453 -108.84656169
-0.61873269 0.78014893 -0.09239861 173.02544428
-0.13412059 0.01098940 0.99090408 40.92544766
Axis 0.08141544 0.18265879 -0.97979962
Axis point 198.28970282 243.37991178 0.00000000
Rotation angle (degrees) 39.41561211
Shift along axis -17.35591133
> volume #8 level 0.008395
> volume #8 level 0.007367
> volume #8 level 0.006339
> volume #8 level 0.005928
> volume #8 level 0.0049
> volume #8 level 0.004694
> volume #8 level 0.004283
> volume #8 level 0.004077
> volume #8 level 0.003872
> volume #8 level 0.004077
> ui tool show "Hide Dust"
> surface dust #8 size 50.34
> view matrix models
> #4,0.82107,0.52004,0.23539,-116.39,-0.48014,0.85219,-0.20793,141.63,-0.30873,0.057706,0.9494,74.429,#7,-0.25498,0.77694,-0.57563,159.72,-0.48539,-0.61771,-0.61873,164.29,-0.83629,0.12164,0.53462,194.97
> view matrix models
> #4,0.78554,0.61095,0.098306,-102.93,-0.60821,0.79156,-0.059316,151.7,-0.11405,-0.013196,0.99339,42.954,#7,-0.21581,0.67608,-0.70451,158.32,-0.59736,-0.66215,-0.45245,167.16,-0.77239,0.32321,0.54677,193.9
> fitmap #1 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
using 10173 atoms
average map value = 0.01768, steps = 48
shifted from previous position = 0.0285
rotated from previous position = 0.0236 degrees
atoms outside contour = 97, contour level = 0.0040773
Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.77413240 0.62548017 0.09743502 -108.78348482
-0.61871031 0.78015823 -0.09246993 173.04062336
-0.13385284 0.01129992 0.99093679 40.84496958
Axis 0.08172445 0.18215188 -0.97986826
Axis point 198.35850392 243.27675668 0.00000000
Rotation angle (degrees) 39.41081833
Shift along axis -17.39328493
> fitmap #4 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
using 104236 atoms
average map value = 0.0104, steps = 108
shifted from previous position = 14.3
rotated from previous position = 5.98 degrees
atoms outside contour = 34631, contour level = 0.0040773
Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.81103895 0.56883502 0.13653773 -110.00386069
-0.55348062 0.82172712 -0.13573415 163.72215947
-0.18940709 0.03451469 0.98129186 49.38976006
Axis 0.14415361 0.27598498 -0.95029050
Axis point 220.17547445 262.06246433 0.00000000
Rotation angle (degrees) 36.19334027
Shift along axis -17.60721577
> fitmap #7 inMap #8
Fit molecule fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) to map postprocess
1.mrc (#8) using 17262 atoms
average map value = 0.01325, steps = 108
shifted from previous position = 13
rotated from previous position = 1.77 degrees
atoms outside contour = 2973, contour level = 0.0040773
Position of fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) relative to
postprocess 1.mrc (#8) coordinates:
Matrix rotation and translation
-0.22927120 0.66107322 -0.71443470 152.80411903
-0.57591627 -0.68385311 -0.44795691 178.76428159
-0.78470070 0.30875094 0.53751064 191.73888093
Axis 0.52122493 0.04839965 -0.85204580
Axis point 181.08241586 46.38734422 0.00000000
Rotation angle (degrees) 133.45675049
Shift along axis -75.07286549
> volume #8 style mesh
> hide #!4 models
> select subtract #4
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #8 style surface
> volume #8 step 1
> volume #8 level 0.0045
> volume #8 level 0.0035
> volume #8 style mesh
> show #!4 models
> volume #8 level 0.0045
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #4
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #4
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel orange
> select clear
> select add #4
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> view matrix models #4,1,0,0,-20.338,0,1,0,1.5317,0,0,1,-2.6363
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.73417,-0.011715,0.67887,-110.65,0.039726,0.99888,-0.025724,-0.60366,-0.67781,0.045854,0.73381,179.35
> view matrix models
> #4,0.9789,0.11074,-0.17176,-3.8946,-0.04979,0.94437,0.32509,-46.014,0.1982,-0.30968,0.92995,41.92
> view matrix models
> #4,0.017369,0.56222,-0.82681,227.8,0.33544,0.77573,0.53453,-130.18,0.9419,-0.28663,-0.17512,126.11
> view matrix models
> #4,-0.12811,0.98357,-0.12718,12.586,0.92087,0.07036,-0.38347,107.6,-0.36822,-0.16624,-0.91476,519.17
> view matrix models
> #4,0.5569,0.82779,0.068008,-131.09,0.01997,0.068512,-0.99745,419.38,-0.83034,0.55683,0.021623,248.94
> view matrix models
> #4,0.84123,0.44504,-0.30702,-21.878,-0.53641,0.61579,-0.57712,317.96,-0.067779,0.65018,0.75675,-81.698
> view matrix models
> #4,0.73797,0.6641,0.11988,-141.84,-0.62927,0.74137,-0.23323,234.59,-0.24376,0.096676,0.965,31.9
> view matrix models
> #4,0.73797,0.6641,0.11988,-108.61,-0.62927,0.74137,-0.23323,201.59,-0.24376,0.096676,0.965,35.063
> view matrix models
> #4,0.72535,0.63548,0.26463,-130.83,-0.54471,0.76491,-0.34381,203.26,-0.42091,0.10523,0.90098,82.196
> fitmap #4 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
using 104236 atoms
average map value = 0.0104, steps = 216
shifted from previous position = 20.7
rotated from previous position = 15.2 degrees
atoms outside contour = 38093, contour level = 0.0045
Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.81109770 0.56879176 0.13636883 -109.97657823
-0.55342535 0.82174938 -0.13582465 163.71638992
-0.18931694 0.03469710 0.98130281 49.31254596
Axis 0.14440007 0.27579500 -0.95030823
Axis point 220.19825708 262.01584691 0.00000000
Rotation angle (degrees) 36.18887777
Shift along axis -17.59058130
> select clear
> select #4/p:724
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
214 atoms, 217 bonds, 24 residues, 1 model selected
> select up
292 atoms, 298 bonds, 33 residues, 1 model selected
> select up
5114 atoms, 5246 bonds, 647 residues, 1 model selected
> select up
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> select up
184767 atoms, 198033 bonds, 15475 residues, 9 models selected
> select down
104236 atoms, 109969 bonds, 10152 residues, 2 models selected
> select down
5114 atoms, 5246 bonds, 647 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/r:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
2019 atoms, 2064 bonds, 258 residues, 1 model selected
> select up
2043 atoms, 2088 bonds, 261 residues, 1 model selected
> select up
2606 atoms, 2669 bonds, 330 residues, 1 model selected
> select up
99122 atoms, 104723 bonds, 9505 residues, 1 model selected
> select down
2606 atoms, 2669 bonds, 330 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/o:843
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
225 atoms, 224 bonds, 45 residues, 1 model selected
> select up
280 atoms, 279 bonds, 56 residues, 1 model selected
> select up
285 atoms, 283 bonds, 57 residues, 1 model selected
> select up
387 atoms, 385 bonds, 78 residues, 1 model selected
> select add #4/q:89
396 atoms, 393 bonds, 79 residues, 1 model selected
> select up
487 atoms, 486 bonds, 89 residues, 1 model selected
> select up
779 atoms, 784 bonds, 127 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/D:158
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> select ~sel & ##selected
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> volume #8 style surface
> volume #8
> volume #8 style mesh
> volume #8 style surface
> volume #8 level 0.004
> volume #8 style mesh
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_FL_map.cxs"
\u2014\u2014\u2014 End of log from Fri Jun 14 15:32:28 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/emd_17297.map.gz"
File reader requires uncompressed file; 'D:/PhD common folder/OneDrive -
Indian Institute of Science/Yeast_project/40S_4B/emd_17297.map.gz' is
compressed
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/emd_17297.map"
Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
0.0109, step 2, values float32
> hide #!8 models
> hide #!4 models
> hide #7 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #9 level 0.002703
> ui tool show "Hide Dust"
> surface dust #9 size 61.82
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/8oz0.cif"
8oz0.cif title:
Structure of a human 48S translation initiation complex with eIF4F and eIF4A
[more info...]
Chain information for 8oz0.cif #10
---
Chain | Description | UniProt
1 3 | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406
2 | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 196-1599
5 | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445
6 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357
7 | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320
8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352
9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25
A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382
B | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218
C | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374
D | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315
E | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
F | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144
H | Eukaryotic translation initiation factor 5 | IF5_HUMAN 1-431
I | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814
J | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913
K | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564
L | 40S ribosomal protein S7 | RS7_HUMAN 1-194
M | 40S ribosomal protein S27 | RS27_HUMAN 1-84
N | 40S ribosomal protein S21 | RS21_HUMAN 1-83
O | 40S ribosomal protein S2 | RS2_HUMAN 1-293
P | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
Q | 40S ribosomal protein SA | RSSA_HUMAN 1-295
R | 40S ribosomal protein S26 | RS26_HUMAN 1-115
S | 40S ribosomal protein S6 | RS6_HUMAN 1-249
T | 40S ribosomal protein S14 | RS14_HUMAN 1-151
U | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333
V | 40S ribosomal protein S13 | RS13_HUMAN 1-151
W | 18S rRNA |
X | 40S ribosomal protein S11 | RS11_HUMAN 1-158
Y | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
Z | 40S ribosomal protein S9 | RS9_HUMAN 1-194
a | 40S ribosomal protein S23 | RS23_HUMAN 1-143
b | 40S ribosomal protein S30 | RS30_HUMAN 75-133
c | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
d | 40S ribosomal protein S8 | RS8_HUMAN 1-208
e | 40S ribosomal protein S24 | RS24_HUMAN 1-133
f | 40S ribosomal protein S5 | RS5_HUMAN 1-204
g | 40S ribosomal protein S16 | RS16_HUMAN 1-146
h | 40S ribosomal protein S3 | RS3_HUMAN 1-243
i | 40S ribosomal protein S10 | RS10_HUMAN 1-165
j | 40S ribosomal protein S15 | RS15_HUMAN 1-145
k | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
l | 40S ribosomal protein S19 | RS19_HUMAN 1-145
m | 40S ribosomal protein S25 | RS25_HUMAN 1-125
n | Small ribosomal subunit protein uS13 | RS18_HUMAN 1-151
o | 40S ribosomal protein S29 | RS29_HUMAN 1-56
p | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156
q | 40S ribosomal protein S12 | RS12_HUMAN 1-132
s | 40S ribosomal protein S28 | RS28_HUMAN 1-69
v | 40S ribosomal protein S17 | RS17_HUMAN 1-135
w | 40S ribosomal protein S20 | RS20_HUMAN 1-119
x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548
y | tRNAiMet |
z | mRNA |
Non-standard residues in 8oz0.cif #10
---
5MC \u2014 5-methylcytidine-5'-monophosphate
5MU \u2014 5-methyluridine 5'-monophosphate
6MZ \u2014 N6-methyladenosine-5'-monophosphate
A2M \u2014 2'-O-methyladenosine 5'-(dihydrogen phosphate)
C4J \u2014
(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-
L-arabinitol
JMH \u2014 3-Methylcytidine- 5'-monophosphate
MA6 \u2014 6N-dimethyladenosine-5'-monophoshate
MG \u2014 magnesium ion
OMC \u2014 O2'-methylycytidine-5'-monophosphate
OMG \u2014 O2'-methylguanosine-5'-monophosphate
OMU \u2014 O2'-methyluridine 5'-monophosphate
UR3 \u2014 3-methyluridine-5'-monophoshate
ZN \u2014 zinc ion
> volume #9 style mesh
> show #!10 cartoons
> hide #!10 atoms
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> volume #9 level 0.00561
> show #7 models
> hide #!9 models
> hide #!10 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> show sel cartoons
> select subtract #7
Nothing selected
> show #!9 models
> show #!10 models
> ui tool show Matchmaker
> matchmaker #7 to #10
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 8oz0.cif, chain W (#10) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2518.7
RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
4.015)
> matchmaker #7 to #10
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 8oz0.cif, chain W (#10) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2518.7
RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
4.015)
> volume #9 level 0.00408
> hide #!9 models
> color #10 magenta
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> select #7/E:207
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> ui tool show "Color Actions"
> color sel beige
> color sel wheat
> color sel navajo white
> select clear
> show #!10 models
> hide #!10 models
> select #7/B:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
188 atoms, 191 bonds, 22 residues, 1 model selected
> select up
1847 atoms, 1874 bonds, 237 residues, 1 model selected
> select clear
> select #7/C:34
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
130 atoms, 129 bonds, 17 residues, 1 model selected
> select up
936 atoms, 948 bonds, 117 residues, 1 model selected
> select up
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select down
936 atoms, 948 bonds, 117 residues, 1 model selected
> color sel pale green
> color sel medium spring green
> color sel chartreuse
> select clear
> select #7/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 13 residues, 1 model selected
> select up
1847 atoms, 1874 bonds, 237 residues, 1 model selected
> color sel orange
> color sel peru
> color sel light salmon
> color sel dark salmon
> color sel coral
> select clear
> select #7/E:71
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> color sel beige
> select clear
> select #7/D:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
91 atoms, 93 bonds, 12 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> color sel magenta
> select clear
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> ui tool show "Side View"
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Fig_5A.jpg" width 957 height 596
> supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain #7/D
Alignment identifier is 7/D
> select #7/D:89
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/D:89-436
2776 atoms, 2834 bonds, 348 residues, 1 model selected
> cartoon hide sel
> show #!8 models
> show #!1 models
> hide #!1 models
> show #2 models
> hide #2 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #7 to #4
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 PIN_5_real_space_refined.pdb, chain 2 (#4) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2881
RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
1.026)
> hide #!4 models
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> transparency sel 30
> transparency sel 0
> transparency #8 50
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> transparency #8 20
> transparency #8 80
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/8i7j.pdb"
8i7j.pdb title:
Yeast 40S-EIF4B - partially open conformation of the 40S head [more info...]
Chain information for 8i7j.pdb #11
---
Chain | Description | UniProt
2 | RNA (1780-mer) |
A | 40S ribosomal protein S0 | RSSA_KLULA 1-254
B | 40S ribosomal protein S1 | RS3A_KLULA 1-255
C | KLLA0F09812P | Q6CKL3_KLULA 1-259
D | KLLA0D08305P | Q6CRK7_KLULA 1-237
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 1-261
F | KLLA0D10659P | Q6CRA3_KLULA 1-227
G | 40S ribosomal protein S6 | RS6_KLULC 1-236
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 1-190
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 1-201
J | KLLA0E23673P | Q6CM18_KLULA 1-188
K | KLLA0B08173P | Q6CVZ5_KLULA 1-106
L | KLLA0A10483P | Q6CX80_KLULA 1-156
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 1-134
N | KLLA0F18040P | Q6CJK0_KLULA 1-151
O | RP59 | RS14_KLULC 1-137
P | KLLA0F07843P | Q6CKV4_KLULA 1-142
Q | 40S ribosomal protein S16 | RS16_KLULC 1-143
R | KLLA0B01474P | Q6CWU3_KLULA 1-136
S | KLLA0B01562P | Q6CWT9_KLULA 1-146
T | KLLA0A07194P | Q6CXM0_KLULA 1-144
U | KLLA0F25542P | Q6CIM1_KLULA 4-120
V | 40S ribosomal protein S21 | RS21_KLULC 1-87
W | KLLA0B07931P | Q6CW06_KLULA 1-130
X | KLLA0B11231P | F2Z602_KLULA 1-145
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 1-135
Z | 40S ribosomal protein S25 | Q6CW78_KLULA 1-108
a | 40S ribosomal protein S26 | Q6CS01_KLULA 1-119
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 1-82
c | S33 | RS28_KLULC 1-67
d | 40S ribosomal protein S29 | RS29_KLULC 1-56
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 1-63
f | ubiquitin-40S ribosomal protein S27A | RS27A_KLULC 1-150
g | KLLA0E12277P | Q6CNI7_KLULA 1-326
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
Non-standard residues in 8i7j.pdb #11
---
MG \u2014 magnesium ion
ZN \u2014 zinc ion
> select add #11
79075 atoms, 84250 bonds, 12 pseudobonds, 7007 residues, 3 models selected
> select add #7
93561 atoms, 100008 bonds, 12 pseudobonds, 8032 residues, 3 models selected
> select subtract #7
76299 atoms, 81416 bonds, 12 pseudobonds, 6659 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> hide #7 models
> ui tool show "Fit in Map"
> fitmap #11 inMap #8
Fit molecule 8i7j.pdb (#11) to map postprocess 1.mrc (#8) using 76299 atoms
average map value = 0.01715, steps = 124
shifted from previous position = 6.85
rotated from previous position = 9.78 degrees
atoms outside contour = 4764, contour level = 0.004
Position of 8i7j.pdb (#11) relative to postprocess 1.mrc (#8) coordinates:
Matrix rotation and translation
0.99574639 -0.08528090 0.03487557 11.36946753
0.08939706 0.98586789 -0.14167806 8.39268741
-0.02230027 0.14419319 0.98929825 -24.08267778
Axis 0.84114773 0.16823422 0.51397252
Axis point 0.00000000 165.31387249 44.41337612
Rotation angle (degrees) 9.78370709
Shift along axis -1.40249549
> ui tool show Matchmaker
> matchmaker #7 to #11
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 8i7j.pdb, chain 2 (#11) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2911.1
RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
1.708)
> matchmaker #7 to #11
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 8i7j.pdb, chain 2 (#11) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2911.1
RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
1.708)
> show #7 models
> hide #!11 models
> transparency #8 90
> transparency #8 95
> transparency #8 99
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Figure_session.cxs"
\u2014\u2014\u2014 End of log from Fri Jul 5 12:41:39 2024 \u2014\u2014\u2014
opened ChimeraX session
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> transparency #7-8 50
> transparency #7-8 0
> transparency #7-8 90
> volume #8 color #b8fbfb
> volume #8 color #ffaa7f
> volume #8 color #c42b1c
> volume #8 color white
> volume #8 color #f3f3f3
> volume #8 color #ffd88f
> volume #8 color #f3f3f3
> volume #8 color #c42b1c
> volume #8 color #ededed
> volume #8 color #f3f3f3
> volume #8 color white
[Repeated 1 time(s)]
> volume #8 color #828282
> volume #8 color #f6f6d3
> close session
QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0)
QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0)
QWindowsWindow::setGeometry: Unable to set geometry 1x1-999883248+545 (frame:
1x1-999883248+545) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
1x1-32768+545 (frame: 1x1-32768+545) margins: 0, 0, 0, 0)
QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0)
QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0)
[deleted to fit within ticket size limits]
> ui tool show "Show Sequence Viewer"
> sequence chain /2
Alignment identifier is 1/2
> select /2:1150
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /2:1150-1157
175 atoms, 196 bonds, 8 residues, 1 model selected
> select /2:1150
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /2:1150-1626
10173 atoms, 11370 bonds, 477 residues, 1 model selected
> select ~sel & ##selected
94063 atoms, 98599 bonds, 9675 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select protein
Nothing selected
> show cartoons
> hide atoms
> set bgColor white
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/fold_40s_rrna_head_2024_06_12_22_44_model_0.cif"
Chain information for fold_40s_rrna_head_2024_06_12_22_44_model_0.cif #2
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_40s_rrna_head_2024_06_12_22_44_model_0.cif, chain A (#2), sequence
alignment score = 1887
RMSD between 441 pruned atom pairs is 0.742 angstroms; (across all 477 pairs:
1.140)
> select add #2
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> hide sel atoms
> select subtract #2
Nothing selected
> lighting soft
> graphics silhouettes true
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder/fold_2024_06_13_01_16_model_0.cif"
Chain information for fold_2024_06_13_01_16_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
> ui tool show Matchmaker
> matchmaker #3 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
1887
RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
1.036)
> matchmaker #3 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
1887
RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
1.036)
> select add #3
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> hide sel atoms
> select subtract #3
Nothing selected
> hide #2 models
> select add #1
10173 atoms, 11370 bonds, 477 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> surface sel
> hide sel atoms
> surface hidePatches (#!1 & sel)
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> select add #4
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select subtract #1
104236 atoms, 109969 bonds, 10152 residues, 2 models selected
> surface hidePatches sel
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #!4 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#4), sequence alignment score = 5525.6
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)
> select clear
> color #4 yellow
> select #1/2:1361
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10173 atoms, 11370 bonds, 477 residues, 2 models selected
> select clear
> select #1/2:1373
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
10173 atoms, 11370 bonds, 477 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> select add #4/U:47
10180 atoms, 11376 bonds, 478 residues, 3 models selected
> select up
10332 atoms, 11529 bonds, 497 residues, 3 models selected
> select up
11018 atoms, 12227 bonds, 583 residues, 3 models selected
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select add #4/D:126
11025 atoms, 12233 bonds, 584 residues, 3 models selected
> select up
11150 atoms, 12360 bonds, 600 residues, 3 models selected
> select up
12792 atoms, 14027 bonds, 810 residues, 3 models selected
> select up
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select down
12792 atoms, 14027 bonds, 810 residues, 3 models selected
> show #3 models
> hide #3 models
> select add #4/K:16
12803 atoms, 14038 bonds, 811 residues, 3 models selected
> select up
12934 atoms, 14172 bonds, 826 residues, 3 models selected
> select up
13601 atoms, 14858 bonds, 906 residues, 3 models selected
> select up
114409 atoms, 121339 bonds, 10629 residues, 3 models selected
> select down
13601 atoms, 14858 bonds, 906 residues, 3 models selected
> select add #4/2:1333
13621 atoms, 14879 bonds, 907 residues, 3 models selected
> select up
51413 atoms, 57141 bonds, 2686 residues, 3 models selected
> select ~sel & ##selected
62996 atoms, 64198 bonds, 7943 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> select clear
> show #3 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/New folder
> (2)/fold_2024_06_13_14_34_model_0.cif"
Chain information for fold_2024_06_13_14_34_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> select #5/C:45@O
1 atom, 1 residue, 1 model selected
> select #5/C:45@O
1 atom, 1 residue, 1 model selected
> select clear
> select add #5
14573 atoms, 15847 bonds, 1035 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> color #5 #ff55ffff
> color #5 red
> ui tool show Matchmaker
> matchmaker #5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
1887
RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
1.027)
> matchmaker #5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
1887
RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
1.027)
> hide #3 models
> select #5/D:61
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 1 model selected
> select up
735 atoms, 749 bonds, 98 residues, 1 model selected
> color sel cyan
> color sel lime
> select clear
> select #5/D:56
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
735 atoms, 749 bonds, 98 residues, 1 model selected
> select ~sel
152248 atoms, 162895 bonds, 12980 residues, 5 models selected
> select subtract #1
142075 atoms, 151525 bonds, 12503 residues, 5 models selected
> select subtract #2
131912 atoms, 140165 bonds, 12026 residues, 3 models selected
> select subtract #3
118074 atoms, 125067 bonds, 11089 residues, 2 models selected
> color sel yellow
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_1-98_AF3.cxs"
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/RRM/fold_rrm_2024_06_13_15_51_model_0.cif"
Chain information for fold_rrm_2024_06_13_15_51_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> select add #6
14522 atoms, 15797 bonds, 1024 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> matchmaker #6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
= 1887
RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
1.122)
> hide #5 models
> show #5 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_1-98_RRM_AF3.cxs"
\u2014\u2014\u2014 End of log from Thu Jun 13 16:35:32 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/fold_4b_fl_2024_06_13_16_47_model_0.cif"
Chain information for fold_4b_fl_2024_06_13_16_47_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
> hide #!4 models
> show #!4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #7 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 1887
RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
1.026)
> matchmaker #7 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
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 PIN_5_real_space_refined.pdb, chain 2 (#1) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C (#7), sequence alignment
score = 3.14629e+230
Fewer than 3 residues aligned; cannot match PIN_5_real_space_refined.pdb,
chain 2 with fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C
> select clear
> show #5 models
> select #7/D:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
91 atoms, 93 bonds, 12 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> color sel red
> select clear
> hide #5 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> select #7/D:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> select ~sel & ##selected
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> color sel yellow
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
\u2014\u2014\u2014 End of log from Thu Jun 13 18:54:25 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/postprocess.mrc"
Opened postprocess.mrc as #8, grid size 360,360,360, pixel 1.2, shown at level
0.0128, step 2, values float32
> volume #8 level 0.005107
> volume #8 level 0.01186
> close #8
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/postprocess 1.mrc"
Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
level 0.0117, step 2, values float32
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select add #4
121498 atoms, 128561 bonds, 11525 residues, 2 models selected
> select subtract #4
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select add #4
121498 atoms, 128561 bonds, 11525 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,1,0,0,29.873,0,1,0,-26.112,0,0,1,-4.1724,#7,0.28189,0.89695,-0.3406,208.48,-0.59451,-0.11535,-0.79578,143.74,-0.75306,0.42681,0.50073,170.55
> view matrix models
> #4,0.82111,0.074806,0.56584,-60.523,0.37786,0.67177,-0.63714,95.401,-0.42778,0.73697,0.52334,8.5864,#7,-0.23912,0.96938,-0.055872,197.7,0.18694,-0.010503,-0.98231,165.67,-0.95282,-0.24534,-0.17871,148.8
> view matrix models
> #4,0.39428,0.28977,0.87211,-82.164,0.12554,0.92311,-0.36347,36.734,-0.91037,0.25279,0.32759,252.6,#7,-0.71788,0.69246,0.071801,189.85,-0.23969,-0.14901,-0.95935,152.45,-0.65361,-0.7059,0.27294,190.17
> view matrix models
> #4,0.93276,0.24233,0.26689,-61.721,-0.20029,0.96394,-0.17522,56.548,-0.29973,0.10998,0.94766,39.262,#7,-0.082117,0.92261,-0.3769,192.67,-0.49758,-0.36563,-0.7866,153.89,-0.86352,0.12294,0.48909,169.98
> view matrix models
> #4,0.90668,0.38695,-0.16792,-3.6645,-0.32198,0.89205,0.31713,0.28806,0.27251,-0.23347,0.9334,5.1958,#7,0.15199,0.69695,-0.70083,194.66,-0.85991,-0.25634,-0.44141,149.71,-0.48729,0.66974,0.56035,177.29
> view matrix models
> #4,0.83083,0.46289,-0.30895,22.476,-0.33038,0.85698,0.39553,-5.67,0.44785,-0.22655,0.86493,-18.087,#7,0.19167,0.55996,-0.80604,195.51,-0.90046,-0.22637,-0.37138,149.99,-0.39042,0.797,0.46084,174.54
> view matrix models
> #4,0.81586,0.41377,-0.40394,53.081,-0.43451,0.8996,0.043887,72.529,0.38154,0.13971,0.91373,-95.845,#7,0.28818,0.51166,-0.80942,198.5,-0.69035,-0.47477,-0.5459,155.39,-0.6636,0.7161,0.2164,155.68
> view matrix models
> #4,0.92225,0.36326,0.13231,-66.698,-0.33704,0.92311,-0.18513,90.197,-0.18939,0.12614,0.97377,7.703,#7,-0.055625,0.84179,-0.53694,182.84,-0.50438,-0.4878,-0.71249,154.45,-0.86169,0.23119,0.45172,165.44
> view matrix models
> #4,0.90839,0.41625,0.039549,-57.795,-0.40792,0.86146,0.30246,24.934,0.091829,-0.29088,0.95234,48.468,#7,-0.021182,0.78365,-0.62084,182.06,-0.8549,-0.33616,-0.39515,151.25,-0.51836,0.52239,0.67706,181.85
> view matrix models
> #4,0.84077,0.51864,-0.15529,-28.698,-0.44574,0.82595,0.34513,31.845,0.30726,-0.22096,0.92562,-4.1938,#7,0.04562,0.62803,-0.77685,182.43,-0.87659,-0.34777,-0.33263,152.83,-0.47907,0.69615,0.53466,174.88
> view matrix models
> #4,0.84077,0.51864,-0.15529,-50.435,-0.44574,0.82595,0.34513,42.879,0.30726,-0.22096,0.92562,-2.874,#7,0.04562,0.62803,-0.77685,160.69,-0.87659,-0.34777,-0.33263,163.86,-0.47907,0.69615,0.53466,176.2
> view matrix models
> #4,0.89894,0.43035,0.081855,-87.056,-0.41583,0.89706,-0.14958,114.17,-0.1378,0.10043,0.98536,2.6161,#7,-0.064087,0.79161,-0.60766,160.9,-0.53788,-0.54029,-0.64712,166.14,-0.84058,0.28538,0.46042,167.22
> view matrix models
> #4,0.82294,0.43483,0.36563,-128.34,-0.25543,0.85805,-0.44554,148.79,-0.50747,0.27326,0.8172,70.448,#7,-0.30188,0.84404,-0.44324,156.38,-0.2466,-0.51824,-0.81891,171.07,-0.9209,-0.13791,0.36459,169
> view matrix models
> #4,0.72434,0.68781,0.047535,-102.66,-0.68702,0.7143,0.13333,154.87,0.057748,-0.12923,0.98993,13.333,#7,-0.24052,0.59065,-0.77025,151.84,-0.71872,-0.64172,-0.26766,176.79,-0.65237,0.48922,0.57886,174.65
> view matrix models
> #4,0.72434,0.68781,0.047535,-93.022,-0.68702,0.7143,0.13333,168.08,0.057748,-0.12923,0.98993,9.714,#7,-0.24052,0.59065,-0.77025,161.48,-0.71872,-0.64172,-0.26766,190,-0.65237,0.48922,0.57886,171.04
> view matrix models
> #4,0.72434,0.68781,0.047535,-95.873,-0.68702,0.7143,0.13333,147.08,0.057748,-0.12923,0.98993,29.062,#7,-0.24052,0.59065,-0.77025,158.63,-0.71872,-0.64172,-0.26766,169,-0.65237,0.48922,0.57886,190.38
> view matrix models
> #4,0.85992,0.49465,-0.12597,-48.976,-0.47438,0.86556,0.16051,68.367,0.18843,-0.078265,0.97896,-5.6566,#7,0.043195,0.66049,-0.74959,166.62,-0.76918,-0.45683,-0.44685,158.7,-0.63758,0.59587,0.4883,185.75
> view matrix models
> #4,0.82107,0.52004,0.23539,-114.53,-0.48014,0.85219,-0.20793,141.5,-0.30873,0.057706,0.9494,68.51,#7,-0.25498,0.77694,-0.57563,161.58,-0.48539,-0.61771,-0.61873,164.17,-0.83629,0.12164,0.53462,189.05
> ui tool show "Fit in Map"
> fitmap #1 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
using 10173 atoms
average map value = 0.01768, steps = 280
shifted from previous position = 37.6
rotated from previous position = 39.4 degrees
atoms outside contour = 1813, contour level = 0.011685
Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.77406817 0.62549730 0.09783453 -108.84656169
-0.61873269 0.78014893 -0.09239861 173.02544428
-0.13412059 0.01098940 0.99090408 40.92544766
Axis 0.08141544 0.18265879 -0.97979962
Axis point 198.28970282 243.37991178 0.00000000
Rotation angle (degrees) 39.41561211
Shift along axis -17.35591133
> volume #8 level 0.008395
> volume #8 level 0.007367
> volume #8 level 0.006339
> volume #8 level 0.005928
> volume #8 level 0.0049
> volume #8 level 0.004694
> volume #8 level 0.004283
> volume #8 level 0.004077
> volume #8 level 0.003872
> volume #8 level 0.004077
> ui tool show "Hide Dust"
> surface dust #8 size 50.34
> view matrix models
> #4,0.82107,0.52004,0.23539,-116.39,-0.48014,0.85219,-0.20793,141.63,-0.30873,0.057706,0.9494,74.429,#7,-0.25498,0.77694,-0.57563,159.72,-0.48539,-0.61771,-0.61873,164.29,-0.83629,0.12164,0.53462,194.97
> view matrix models
> #4,0.78554,0.61095,0.098306,-102.93,-0.60821,0.79156,-0.059316,151.7,-0.11405,-0.013196,0.99339,42.954,#7,-0.21581,0.67608,-0.70451,158.32,-0.59736,-0.66215,-0.45245,167.16,-0.77239,0.32321,0.54677,193.9
> fitmap #1 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
using 10173 atoms
average map value = 0.01768, steps = 48
shifted from previous position = 0.0285
rotated from previous position = 0.0236 degrees
atoms outside contour = 97, contour level = 0.0040773
Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.77413240 0.62548017 0.09743502 -108.78348482
-0.61871031 0.78015823 -0.09246993 173.04062336
-0.13385284 0.01129992 0.99093679 40.84496958
Axis 0.08172445 0.18215188 -0.97986826
Axis point 198.35850392 243.27675668 0.00000000
Rotation angle (degrees) 39.41081833
Shift along axis -17.39328493
> fitmap #4 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
using 104236 atoms
average map value = 0.0104, steps = 108
shifted from previous position = 14.3
rotated from previous position = 5.98 degrees
atoms outside contour = 34631, contour level = 0.0040773
Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.81103895 0.56883502 0.13653773 -110.00386069
-0.55348062 0.82172712 -0.13573415 163.72215947
-0.18940709 0.03451469 0.98129186 49.38976006
Axis 0.14415361 0.27598498 -0.95029050
Axis point 220.17547445 262.06246433 0.00000000
Rotation angle (degrees) 36.19334027
Shift along axis -17.60721577
> fitmap #7 inMap #8
Fit molecule fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) to map postprocess
1.mrc (#8) using 17262 atoms
average map value = 0.01325, steps = 108
shifted from previous position = 13
rotated from previous position = 1.77 degrees
atoms outside contour = 2973, contour level = 0.0040773
Position of fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) relative to
postprocess 1.mrc (#8) coordinates:
Matrix rotation and translation
-0.22927120 0.66107322 -0.71443470 152.80411903
-0.57591627 -0.68385311 -0.44795691 178.76428159
-0.78470070 0.30875094 0.53751064 191.73888093
Axis 0.52122493 0.04839965 -0.85204580
Axis point 181.08241586 46.38734422 0.00000000
Rotation angle (degrees) 133.45675049
Shift along axis -75.07286549
> volume #8 style mesh
> hide #!4 models
> select subtract #4
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #8 style surface
> volume #8 step 1
> volume #8 level 0.0045
> volume #8 level 0.0035
> volume #8 style mesh
> show #!4 models
> volume #8 level 0.0045
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #4
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | 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
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #4
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel orange
> select clear
> select add #4
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> view matrix models #4,1,0,0,-20.338,0,1,0,1.5317,0,0,1,-2.6363
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.73417,-0.011715,0.67887,-110.65,0.039726,0.99888,-0.025724,-0.60366,-0.67781,0.045854,0.73381,179.35
> view matrix models
> #4,0.9789,0.11074,-0.17176,-3.8946,-0.04979,0.94437,0.32509,-46.014,0.1982,-0.30968,0.92995,41.92
> view matrix models
> #4,0.017369,0.56222,-0.82681,227.8,0.33544,0.77573,0.53453,-130.18,0.9419,-0.28663,-0.17512,126.11
> view matrix models
> #4,-0.12811,0.98357,-0.12718,12.586,0.92087,0.07036,-0.38347,107.6,-0.36822,-0.16624,-0.91476,519.17
> view matrix models
> #4,0.5569,0.82779,0.068008,-131.09,0.01997,0.068512,-0.99745,419.38,-0.83034,0.55683,0.021623,248.94
> view matrix models
> #4,0.84123,0.44504,-0.30702,-21.878,-0.53641,0.61579,-0.57712,317.96,-0.067779,0.65018,0.75675,-81.698
> view matrix models
> #4,0.73797,0.6641,0.11988,-141.84,-0.62927,0.74137,-0.23323,234.59,-0.24376,0.096676,0.965,31.9
> view matrix models
> #4,0.73797,0.6641,0.11988,-108.61,-0.62927,0.74137,-0.23323,201.59,-0.24376,0.096676,0.965,35.063
> view matrix models
> #4,0.72535,0.63548,0.26463,-130.83,-0.54471,0.76491,-0.34381,203.26,-0.42091,0.10523,0.90098,82.196
> fitmap #4 inMap #8
Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
using 104236 atoms
average map value = 0.0104, steps = 216
shifted from previous position = 20.7
rotated from previous position = 15.2 degrees
atoms outside contour = 38093, contour level = 0.0045
Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
(#8) coordinates:
Matrix rotation and translation
0.81109770 0.56879176 0.13636883 -109.97657823
-0.55342535 0.82174938 -0.13582465 163.71638992
-0.18931694 0.03469710 0.98130281 49.31254596
Axis 0.14440007 0.27579500 -0.95030823
Axis point 220.19825708 262.01584691 0.00000000
Rotation angle (degrees) 36.18887777
Shift along axis -17.59058130
> select clear
> select #4/p:724
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
214 atoms, 217 bonds, 24 residues, 1 model selected
> select up
292 atoms, 298 bonds, 33 residues, 1 model selected
> select up
5114 atoms, 5246 bonds, 647 residues, 1 model selected
> select up
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> select up
184767 atoms, 198033 bonds, 15475 residues, 9 models selected
> select down
104236 atoms, 109969 bonds, 10152 residues, 2 models selected
> select down
5114 atoms, 5246 bonds, 647 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/r:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
2019 atoms, 2064 bonds, 258 residues, 1 model selected
> select up
2043 atoms, 2088 bonds, 261 residues, 1 model selected
> select up
2606 atoms, 2669 bonds, 330 residues, 1 model selected
> select up
99122 atoms, 104723 bonds, 9505 residues, 1 model selected
> select down
2606 atoms, 2669 bonds, 330 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/o:843
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
225 atoms, 224 bonds, 45 residues, 1 model selected
> select up
280 atoms, 279 bonds, 56 residues, 1 model selected
> select up
285 atoms, 283 bonds, 57 residues, 1 model selected
> select up
387 atoms, 385 bonds, 78 residues, 1 model selected
> select add #4/q:89
396 atoms, 393 bonds, 79 residues, 1 model selected
> select up
487 atoms, 486 bonds, 89 residues, 1 model selected
> select up
779 atoms, 784 bonds, 127 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/D:158
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
44 atoms, 43 bonds, 6 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> select ~sel & ##selected
13838 atoms, 15098 bonds, 937 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> volume #8 style surface
> volume #8
> volume #8 style mesh
> volume #8 style surface
> volume #8 level 0.004
> volume #8 style mesh
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/40S_4B_FL_map.cxs"
\u2014\u2014\u2014 End of log from Fri Jun 14 15:32:28 2024 \u2014\u2014\u2014
opened ChimeraX session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/emd_17297.map.gz"
File reader requires uncompressed file; 'D:/PhD common folder/OneDrive -
Indian Institute of Science/Yeast_project/40S_4B/emd_17297.map.gz' is
compressed
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/emd_17297.map"
Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
0.0109, step 2, values float32
> hide #!8 models
> hide #!4 models
> hide #7 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #9 level 0.002703
> ui tool show "Hide Dust"
> surface dust #9 size 61.82
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/8oz0.cif"
8oz0.cif title:
Structure of a human 48S translation initiation complex with eIF4F and eIF4A
[more info...]
Chain information for 8oz0.cif #10
---
Chain | Description | UniProt
1 3 | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406
2 | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 196-1599
5 | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445
6 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357
7 | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320
8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352
9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25
A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382
B | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218
C | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374
D | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315
E | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
F | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325
G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144
H | Eukaryotic translation initiation factor 5 | IF5_HUMAN 1-431
I | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814
J | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913
K | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564
L | 40S ribosomal protein S7 | RS7_HUMAN 1-194
M | 40S ribosomal protein S27 | RS27_HUMAN 1-84
N | 40S ribosomal protein S21 | RS21_HUMAN 1-83
O | 40S ribosomal protein S2 | RS2_HUMAN 1-293
P | 40S ribosomal protein S3a | RS3A_HUMAN 1-264
Q | 40S ribosomal protein SA | RSSA_HUMAN 1-295
R | 40S ribosomal protein S26 | RS26_HUMAN 1-115
S | 40S ribosomal protein S6 | RS6_HUMAN 1-249
T | 40S ribosomal protein S14 | RS14_HUMAN 1-151
U | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333
V | 40S ribosomal protein S13 | RS13_HUMAN 1-151
W | 18S rRNA |
X | 40S ribosomal protein S11 | RS11_HUMAN 1-158
Y | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263
Z | 40S ribosomal protein S9 | RS9_HUMAN 1-194
a | 40S ribosomal protein S23 | RS23_HUMAN 1-143
b | 40S ribosomal protein S30 | RS30_HUMAN 75-133
c | 40S ribosomal protein S15a | RS15A_HUMAN 1-130
d | 40S ribosomal protein S8 | RS8_HUMAN 1-208
e | 40S ribosomal protein S24 | RS24_HUMAN 1-133
f | 40S ribosomal protein S5 | RS5_HUMAN 1-204
g | 40S ribosomal protein S16 | RS16_HUMAN 1-146
h | 40S ribosomal protein S3 | RS3_HUMAN 1-243
i | 40S ribosomal protein S10 | RS10_HUMAN 1-165
j | 40S ribosomal protein S15 | RS15_HUMAN 1-145
k | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317
l | 40S ribosomal protein S19 | RS19_HUMAN 1-145
m | 40S ribosomal protein S25 | RS25_HUMAN 1-125
n | Small ribosomal subunit protein uS13 | RS18_HUMAN 1-151
o | 40S ribosomal protein S29 | RS29_HUMAN 1-56
p | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156
q | 40S ribosomal protein S12 | RS12_HUMAN 1-132
s | 40S ribosomal protein S28 | RS28_HUMAN 1-69
v | 40S ribosomal protein S17 | RS17_HUMAN 1-135
w | 40S ribosomal protein S20 | RS20_HUMAN 1-119
x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548
y | tRNAiMet |
z | mRNA |
Non-standard residues in 8oz0.cif #10
---
5MC \u2014 5-methylcytidine-5'-monophosphate
5MU \u2014 5-methyluridine 5'-monophosphate
6MZ \u2014 N6-methyladenosine-5'-monophosphate
A2M \u2014 2'-O-methyladenosine 5'-(dihydrogen phosphate)
C4J \u2014
(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-
L-arabinitol
JMH \u2014 3-Methylcytidine- 5'-monophosphate
MA6 \u2014 6N-dimethyladenosine-5'-monophoshate
MG \u2014 magnesium ion
OMC \u2014 O2'-methylycytidine-5'-monophosphate
OMG \u2014 O2'-methylguanosine-5'-monophosphate
OMU \u2014 O2'-methyluridine 5'-monophosphate
UR3 \u2014 3-methyluridine-5'-monophoshate
ZN \u2014 zinc ion
> volume #9 style mesh
> show #!10 cartoons
> hide #!10 atoms
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> volume #9 level 0.00561
> show #7 models
> hide #!9 models
> hide #!10 models
> select add #7
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> show sel cartoons
> select subtract #7
Nothing selected
> show #!9 models
> show #!10 models
> ui tool show Matchmaker
> matchmaker #7 to #10
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 8oz0.cif, chain W (#10) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2518.7
RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
4.015)
> matchmaker #7 to #10
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 8oz0.cif, chain W (#10) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2518.7
RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
4.015)
> volume #9 level 0.00408
> hide #!9 models
> color #10 magenta
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> select #7/E:207
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> ui tool show "Color Actions"
> color sel beige
> color sel wheat
> color sel navajo white
> select clear
> show #!10 models
> hide #!10 models
> select #7/B:25
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
188 atoms, 191 bonds, 22 residues, 1 model selected
> select up
1847 atoms, 1874 bonds, 237 residues, 1 model selected
> select clear
> select #7/C:34
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
130 atoms, 129 bonds, 17 residues, 1 model selected
> select up
936 atoms, 948 bonds, 117 residues, 1 model selected
> select up
17262 atoms, 18592 bonds, 1373 residues, 1 model selected
> select down
936 atoms, 948 bonds, 117 residues, 1 model selected
> color sel pale green
> color sel medium spring green
> color sel chartreuse
> select clear
> select #7/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
99 atoms, 99 bonds, 13 residues, 1 model selected
> select up
1847 atoms, 1874 bonds, 237 residues, 1 model selected
> color sel orange
> color sel peru
> color sel light salmon
> color sel dark salmon
> color sel coral
> select clear
> select #7/E:71
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
10163 atoms, 11360 bonds, 477 residues, 1 model selected
> color sel beige
> select clear
> select #7/D:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
91 atoms, 93 bonds, 12 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> color sel magenta
> select clear
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> ui tool show "Side View"
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Fig_5A.jpg" width 957 height 596
> supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain #7/D
Alignment identifier is 7/D
> select #7/D:89
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/D:89-436
2776 atoms, 2834 bonds, 348 residues, 1 model selected
> cartoon hide sel
> show #!8 models
> show #!1 models
> hide #!1 models
> show #2 models
> hide #2 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #7 to #4
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 PIN_5_real_space_refined.pdb, chain 2 (#4) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2881
RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
1.026)
> hide #!4 models
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> transparency sel 30
> transparency sel 0
> transparency #8 50
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> transparency #8 20
> transparency #8 80
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/8i7j.pdb"
8i7j.pdb title:
Yeast 40S-EIF4B - partially open conformation of the 40S head [more info...]
Chain information for 8i7j.pdb #11
---
Chain | Description | UniProt
2 | RNA (1780-mer) |
A | 40S ribosomal protein S0 | RSSA_KLULA 1-254
B | 40S ribosomal protein S1 | RS3A_KLULA 1-255
C | KLLA0F09812P | Q6CKL3_KLULA 1-259
D | KLLA0D08305P | Q6CRK7_KLULA 1-237
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 1-261
F | KLLA0D10659P | Q6CRA3_KLULA 1-227
G | 40S ribosomal protein S6 | RS6_KLULC 1-236
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 1-190
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 1-201
J | KLLA0E23673P | Q6CM18_KLULA 1-188
K | KLLA0B08173P | Q6CVZ5_KLULA 1-106
L | KLLA0A10483P | Q6CX80_KLULA 1-156
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 1-134
N | KLLA0F18040P | Q6CJK0_KLULA 1-151
O | RP59 | RS14_KLULC 1-137
P | KLLA0F07843P | Q6CKV4_KLULA 1-142
Q | 40S ribosomal protein S16 | RS16_KLULC 1-143
R | KLLA0B01474P | Q6CWU3_KLULA 1-136
S | KLLA0B01562P | Q6CWT9_KLULA 1-146
T | KLLA0A07194P | Q6CXM0_KLULA 1-144
U | KLLA0F25542P | Q6CIM1_KLULA 4-120
V | 40S ribosomal protein S21 | RS21_KLULC 1-87
W | KLLA0B07931P | Q6CW06_KLULA 1-130
X | KLLA0B11231P | F2Z602_KLULA 1-145
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 1-135
Z | 40S ribosomal protein S25 | Q6CW78_KLULA 1-108
a | 40S ribosomal protein S26 | Q6CS01_KLULA 1-119
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 1-82
c | S33 | RS28_KLULC 1-67
d | 40S ribosomal protein S29 | RS29_KLULC 1-56
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 1-63
f | ubiquitin-40S ribosomal protein S27A | RS27A_KLULC 1-150
g | KLLA0E12277P | Q6CNI7_KLULA 1-326
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
Non-standard residues in 8i7j.pdb #11
---
MG \u2014 magnesium ion
ZN \u2014 zinc ion
> select add #11
79075 atoms, 84250 bonds, 12 pseudobonds, 7007 residues, 3 models selected
> select add #7
93561 atoms, 100008 bonds, 12 pseudobonds, 8032 residues, 3 models selected
> select subtract #7
76299 atoms, 81416 bonds, 12 pseudobonds, 6659 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> hide #7 models
> ui tool show "Fit in Map"
> fitmap #11 inMap #8
Fit molecule 8i7j.pdb (#11) to map postprocess 1.mrc (#8) using 76299 atoms
average map value = 0.01715, steps = 124
shifted from previous position = 6.85
rotated from previous position = 9.78 degrees
atoms outside contour = 4764, contour level = 0.004
Position of 8i7j.pdb (#11) relative to postprocess 1.mrc (#8) coordinates:
Matrix rotation and translation
0.99574639 -0.08528090 0.03487557 11.36946753
0.08939706 0.98586789 -0.14167806 8.39268741
-0.02230027 0.14419319 0.98929825 -24.08267778
Axis 0.84114773 0.16823422 0.51397252
Axis point 0.00000000 165.31387249 44.41337612
Rotation angle (degrees) 9.78370709
Shift along axis -1.40249549
> ui tool show Matchmaker
> matchmaker #7 to #11
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 8i7j.pdb, chain 2 (#11) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2911.1
RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
1.708)
> matchmaker #7 to #11
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 8i7j.pdb, chain 2 (#11) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2911.1
RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
1.708)
> show #7 models
> hide #!11 models
> transparency #8 90
> transparency #8 95
> transparency #8 99
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Figure_session.cxs"
> select clear
> select #7/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #7/C:2
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #7/C:4
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #7/C:3
30 atoms, 26 bonds, 4 residues, 1 model selected
> select add #7/C:5
39 atoms, 34 bonds, 5 residues, 1 model selected
> select add #7/C:6
48 atoms, 42 bonds, 6 residues, 1 model selected
> select add #7/C:7
57 atoms, 50 bonds, 7 residues, 1 model selected
> select add #7/C:8
63 atoms, 55 bonds, 8 residues, 1 model selected
> select add #7/C:9
72 atoms, 63 bonds, 9 residues, 1 model selected
> select add #7/C:11
81 atoms, 71 bonds, 10 residues, 1 model selected
> select add #7/C:10
90 atoms, 79 bonds, 11 residues, 1 model selected
> hide sel cartoons
> select #7/A:106
13 atoms, 13 bonds, 1 residue, 1 model selected
> select add #7/A:105
22 atoms, 21 bonds, 2 residues, 1 model selected
> select add #7/A:104
31 atoms, 29 bonds, 3 residues, 1 model selected
> select add #7/A:103
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #7/A:102
44 atoms, 40 bonds, 5 residues, 1 model selected
> select add #7/A:101
51 atoms, 47 bonds, 6 residues, 1 model selected
> select add #7/A:100
62 atoms, 57 bonds, 7 residues, 1 model selected
> select add #7/A:99
71 atoms, 65 bonds, 8 residues, 1 model selected
> select add #7/A:98
79 atoms, 72 bonds, 9 residues, 1 model selected
> select add #7/A:97
83 atoms, 75 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select #7/B:237
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #7/B:236
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #7/B:235
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #7/B:234
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #7/B:233
31 atoms, 26 bonds, 5 residues, 1 model selected
> select add #7/B:232
40 atoms, 34 bonds, 6 residues, 1 model selected
> select add #7/B:231
47 atoms, 40 bonds, 7 residues, 1 model selected
> select add #7/B:230
54 atoms, 47 bonds, 8 residues, 1 model selected
> select add #7/B:229
63 atoms, 55 bonds, 9 residues, 1 model selected
> select add #7/B:228
70 atoms, 61 bonds, 10 residues, 1 model selected
> select add #7/B:227
77 atoms, 68 bonds, 11 residues, 1 model selected
> select add #7/B:226
88 atoms, 78 bonds, 12 residues, 1 model selected
> select add #7/B:225
100 atoms, 90 bonds, 13 residues, 1 model selected
> select add #7/B:224
108 atoms, 97 bonds, 14 residues, 1 model selected
> select add #7/B:223
117 atoms, 105 bonds, 15 residues, 1 model selected
> select add #7/B:222
124 atoms, 111 bonds, 16 residues, 1 model selected
> select add #7/B:221
130 atoms, 116 bonds, 17 residues, 1 model selected
> select add #7/B:220
137 atoms, 123 bonds, 18 residues, 1 model selected
> select add #7/B:219
146 atoms, 131 bonds, 19 residues, 1 model selected
> select add #7/B:218
154 atoms, 138 bonds, 20 residues, 1 model selected
> hide sel cartoons
> transparency #8 90
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Fig_5B.png" width 957 height 596
> supersample 3
> hide #!8 models
> hide #!9 models
> ui tool show "Side View"
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Fig_5C.png" width 957 height 596
> supersample 3
> select #7/A:74
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 89 bonds, 10 residues, 1 model selected
> select up
892 atoms, 916 bonds, 106 residues, 1 model selected
> color sel blue
> select clear
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Fig_5C.png" width 957 height 596
> supersample 3
> show #!9 models
> show #!10 models
> ui tool show Matchmaker
> matchmaker #7 to #10
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 8oz0.cif, chain W (#10) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2518.7
RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
4.015)
> matchmaker #7 to #10
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 8oz0.cif, chain W (#10) with
fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
score = 2518.7
RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
4.015)
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume #8 level 0.006577
> volume #9 level 0.005151
> volume #9 level 0.006376
> select #7/D:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
25 atoms, 24 bonds, 3 residues, 1 model selected
> select up
3424 atoms, 3494 bonds, 436 residues, 1 model selected
> show sel cartoons
> select clear
> transparency #9 90
> transparency #9 50
> volume #8 level 0.005933
> volume #9 level 0.005916
> volume #9 level 0.005304
> show #!10 models
> color #10 yellow
> volume #9 level 0
> volume #9 style surface
> undo
[Repeated 3 time(s)]
> volume #8 style surface
> volume #9 level 0.0008901
> volume #9 level 0
> volume #9 level 0.04
> volume #9 level 0.004
> select clear
> volume #9 level 0.0045
> volume #9 level 0.004
> transparency #9 50
> transparency #9 90
> show #5 models
> hide #5 models
> show #!10 models
> color #10 yellow
> hide #!10 models
> show #!10 models
> hide #7 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/S4A.png" width 957 height 596 supersample
> 3
> show #7 models
> hide #!10 models
> show #!10 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/S4A_1.png" width 957 height 596
> supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/S4A_2.png" width 957 height 596
> supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/4B_FL/Fig_S4.cxs"
\u2014\u2014\u2014 End of log from Fri Jul 5 17:37:19 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!10 models
> hide #7 models
> select add #9
2 models selected
> ui tool show "Color Actions"
> color sel wheat
> select subtract #9
Nothing selected
> show #!10 models
> hide #!9 models
> select #10/W:1309
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
36639 atoms, 40968 bonds, 1716 residues, 1 model selected
> select up
36725 atoms, 40968 bonds, 1802 residues, 1 model selected
> select up
121610 atoms, 127231 bonds, 13795 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> select clear
> show #!9 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select add #10
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> select ~sel & ##selected
Nothing selected
> select add #10
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> select transparency 0.5
Expected an objects specifier or a keyword
> cartoon transparency sel 0.5
Expected an atoms specifier or a keyword
> transparency sel 50 target c
> select subtract #10
Nothing selected
> select add #10
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> transparency sel 10 target c
> transparency sel 0 target c
> transparency sel 1 target c
> transparency sel 0.1 target c
> transparency sel 0.5 target c
> transparency sel 0.2 target c
> select clear
> select add #10
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> ui tool show "Color Actions"
> color sel gainsboro
> color sel papaya whip
> color sel seashell
> color sel cornsilk
> color sel lemon chiffon
> select clear
> select add #10
121610 atoms, 127231 bonds, 1649 pseudobonds, 13795 residues, 4 models
selected
> surface (#!10 & sel)
> surface hidePatches (#!10 & sel)
> select clear
> show #7 models
> hide #7 models
> hide #!9 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/S4A.png" width 957 height 585 supersample 3
> transparentBackground true
> show #!9 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/S4A_1.png" width 957 height 585 supersample 3
> show #!11 models
> hide #!11 models
> show #7 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/S4B.png" width 957 height 585 supersample 3
> transparentBackground true
> hide #!9 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/S4B.png" width 957 height 585 supersample 3
> transparentBackground true
> show #!9 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/S4B_1.png" width 957 height 585 supersample 3
> transparentBackground true
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Yeast_project/40S_4B/fig5C_zoomed.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state
return _copy(data)
^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 220, in _copy
return data.copy()
^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 2.42 MiB for an
array with shape (211230, 3) and data type int32
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000002199E6CED90> -> <chimerax.atomic.molsurf.MolecularSurface object at
0x00000219D6E34890> '8oz0.cif_2 SES surface': Unable to allocate 2.42 MiB for
an array with shape (211230, 3) and data type int32
ValueError: error processing: 'models' -> -> '8oz0.cif_2 SES surface': Unable
to allocate 2.42 MiB for an array with shape (211230, 3) and data type int32
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 310, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state
return _copy(data)
^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\state.py", line 220, in _copy
return data.copy()
^^^^^^^^^^^
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 2.42 MiB for an
array with shape (211230, 3) and data type int32
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 646, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000002199E6CED90> -> <chimerax.atomic.molsurf.MolecularSurface object at
0x00000219D6E34890> '8oz0.cif_2 SES surface': Unable to allocate 2.42 MiB for
an array with shape (211230, 3) and data type int32
ValueError: error processing: 'models' -> -> '8oz0.cif_2 SES surface': Unable
to allocate 2.42 MiB for an array with shape (211230, 3) and data type int32
File "C:\Program Files\ChimeraX 1.9.dev202407300242\bin\Lib\site-
packages\chimerax\core\session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 457.49
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.0, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: windows
Manufacturer: LENOVO
Model: 82B5
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 8,452,902,912
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.7.4
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.14
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.4
ChimeraX-AtomicLibrary: 14.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202407300242
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-Foldseek: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.7
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.5
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.13
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.8
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.2
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.3
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.9.1
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.1.2
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt_toolkit: 3.0.47
psutil: 5.9.8
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject_hooks: 1.1.0
PyQt6-commercial: 6.7.0
PyQt6-Qt6: 6.7.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.2
PyQt6-WebEngineSubwheel-Qt6: 6.7.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.2
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 70.3.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
Sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing_extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.2
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArrayMemoryError saving molecular surface in session |
comment:2 by , 15 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
ChimeraX ran out of memory when trying to save a session. I tried to allocate just 2 Mbytes of memory and got an out of memory error. It is hard to tell how much data was open since the ChimeraX Log is very long. The computer only has 8 GB of memory and Windows is especially prone to running out of memory.
If this was a long session (lots of different files opened and closed) then it may be that ChimeraX did not free all the memory and eventually ran out. Or it may be that there was a lot of data opened. In those situations more than 8 GB of memory may be needed.
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Reported by Prafful Sharma