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Opened 16 months ago
Last modified 16 months ago
#15757 closed defect
ArrayMemoryError saving molecular surface in session — at Version 1
| 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 (1)
comment:1 by , 16 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 |
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Reported by Prafful Sharma