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Opened 7 months ago
Closed 7 months ago
#17120 closed defect (duplicate)
Session restore: ItemTable's selectionModel() is None (Parsing BlastProtein results failed)
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-135-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> open
> /home/miramay/software/calc_level_chimeraX/calc_level_ChimeraX/calc_level.py
/home/miramay/software/calc_level_chimeraX/calc_level_ChimeraX/calc_level.py:96:
FutureWarning: You are using `torch.load` with `weights_only=False` (the
current default value), which uses the default pickle module implicitly. It is
possible to construct malicious pickle data which will execute arbitrary code
during unpickling (See
https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for
more details). In a future release, the default value for `weights_only` will
be flipped to `True`. This limits the functions that could be executed during
unpickling. Arbitrary objects will no longer be allowed to be loaded via this
mode unless they are explicitly allowlisted by the user via
`torch.serialization.add_safe_globals`. We recommend you start setting
`weights_only=True` for any use case where you don't have full control of the
loaded file. Please open an issue on GitHub for any issues related to this
experimental feature.
checkpoint = torch.load(os.path.join(dir, 'weights_5e6.pth'), map_location =
device)
executed calc_level.py
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J393_big_mask/run001_mask/run001_mask.cif
Summary of feedback from opening
/media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J393_big_mask/run001_mask/run001_mask.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for run001_mask.cif #1
---
Chain | Description
5 | No description available
7 | No description available
8 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AL AR | No description available
AO | No description available
AP | No description available
Aj | No description available
Al | No description available
Am | No description available
An | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ BK | No description available
BL | No description available
BM | No description available
BN BP | No description available
BO | No description available
BQ BS | No description available
BR | No description available
BV | No description available
Bb | No description available
Bi | No description available
Bj | No description available
Bk | No description available
Bl | No description available
Bm | No description available
Bn | No description available
Bo | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | 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 X | No description available
W | No description available
Z | No description available
b | No description available
g | No description available
i | No description available
j | No description available
m | No description available
n | No description available
o | No description available
p | No description available
u | No description available
v | No description available
w | No description available
y | No description available
> set bgColor white
> lighting soft
> hide atoms
> show atoms
> show cartoons
Computing secondary structure
> hide atoms
> ui tool show "Show Sequence Viewer"
> select #1/Br
342 atoms, 382 bonds, 16 residues, 1 model selected
> select #1/Br,Bl, Bq,
Expected an objects specifier or a keyword
> select #1/Br,Bl, Bq
603 atoms, 674 bonds, 28 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ,
Expected an objects specifier or a keyword
> select #1/Br,Bl, BQ, BJ
603 atoms, 673 bonds, 28 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ,Bs, BO
872 atoms, 970 bonds, 41 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo
727 atoms, 810 bonds, 34 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu
987 atoms, 1100 bonds, 46 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp
1155 atoms, 1286 bonds, 54 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, Bv
1498 atoms, 1669 bonds, 70 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6
1404 atoms, 1554 bonds, 72 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi
1689 atoms, 1874 bonds, 85 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al,
Expected an objects specifier or a keyword
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao
2187 atoms, 2381 bonds, 149 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq
2670 atoms, 2906 bonds, 184 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt
3067 atoms, 3353 bonds, 202 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk
3221 atoms, 3525 bonds, 209 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, Bn
3304 atoms, 3616 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR
3458 atoms, 3787 bonds, 220 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS
3567 atoms, 3908 bonds, 225 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F
3651 atoms, 3999 bonds, 231 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A
3722 atoms, 4071 bonds, 240 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL
3765 atoms, 4118 bonds, 242 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP
3854 atoms, 4217 bonds, 246 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g
3874 atoms, 4236 bonds, 248 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B
3909 atoms, 4270 bonds, 252 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W
3936 atoms, 4295 bonds, 256 residues, 1 model selected
> hide sel cartoons
> graphics silhouettes true
> open
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/J393_newmask/cryosparc_P249_J393_003_volume_map_sharp.mrc
Opened cryosparc_P249_J393_003_volume_map_sharp.mrc as #2, grid size
440,440,440, pixel 1.06, shown at level 0.319, step 2, values float32
> surface dust #2 size 10.6
> volume #2 step 1
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2 #d4d4d4dc models
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view
> show #!2 models
> color #2 #b2b2b2ff models
> hide #1 models
> show #1 models
> hide #!2 models
> open /home/miramay/Downloads/AF-P0A6M8-F1-model_v4.pdb
AF-P0A6M8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for elongation factor G (P0A6M8) [more
info...]
Chain information for AF-P0A6M8-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | elongation factor G | EFG_ECOLI 1-704
Computing secondary structure
> select add #3
9389 atoms, 9850 bonds, 960 residues, 2 models selected
> view
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,15.61,0,1,0,15.376,0,0,1,14.334,#3,1,0,0,15.61,0,1,0,15.376,0,0,1,14.334
> show #!2 models
> view matrix models
> #1,1,0,0,123.75,0,1,0,109.31,0,0,1,74.232,#3,1,0,0,123.75,0,1,0,109.31,0,0,1,74.232
> undo
> select add #1
15300 atoms, 15792 bonds, 1666 residues, 2 models selected
> select subtract #1
5453 atoms, 5555 bonds, 704 residues, 1 model selected
> view matrix models #3,1,0,0,316.07,0,1,0,262.8,0,0,1,138.24
> show #!2 models
> select add #1
15300 atoms, 15792 bonds, 1666 residues, 2 models selected
> select subtract #1
5453 atoms, 5555 bonds, 704 residues, 1 model selected
> view matrix models #3,1,0,0,115.88,0,1,0,213.66,0,0,1,417.04
> view matrix models #3,1,0,0,230.63,0,1,0,434.74,0,0,1,502.5
> view matrix models #3,1,0,0,180.5,0,1,0,326.52,0,0,1,430.54
> view matrix models #3,1,0,0,403.23,0,1,0,209.56,0,0,1,340.85
> view matrix models #3,1,0,0,336.41,0,1,0,241.52,0,0,1,183.55
> view matrix models #3,1,0,0,378.51,0,1,0,304.13,0,0,1,208.23
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.12948,-0.02524,0.99126,395.79,-0.85059,0.51098,0.12411,316.29,-0.50964,-0.85922,0.044691,209.77
> view matrix models
> #3,0.15124,-0.45623,0.87692,397.01,-0.96944,0.1049,0.22178,320.6,-0.19317,-0.88366,-0.42642,202.71
> hide #!2 models
> view matrix models
> #3,-0.2273,-0.38327,0.89523,400.46,-0.93073,0.35594,-0.083926,316.14,-0.28648,-0.8523,-0.43763,203.35
> view matrix models
> #3,-0.3407,-0.34064,0.87629,401.17,-0.88663,0.42646,-0.17894,314.49,-0.31275,-0.83791,-0.44731,203.44
> view matrix models
> #3,-0.11501,-0.41553,0.90228,399.61,-0.95883,0.28386,0.0085134,317.63,-0.25966,-0.86415,-0.43107,203.21
> view matrix models
> #3,-0.20143,-0.30424,0.93105,400.08,-0.91572,0.39589,-0.068749,315.9,-0.34768,-0.86643,-0.35835,204.72
> view matrix models
> #3,-0.28238,-0.16526,0.94496,400.21,-0.8476,0.50431,-0.16509,313.79,-0.44927,-0.84756,-0.28248,206.27
> view matrix models
> #3,0.0093669,0.0045308,0.99995,396.87,-0.9981,-0.060869,0.0096254,319.97,0.060909,-0.99814,0.003952,204.61
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.0093669,0.0045308,0.99995,284.08,-0.9981,-0.060869,0.0096254,260.64,0.060909,-0.99814,0.003952,191.71
> view matrix models
> #3,0.0093669,0.0045308,0.99995,283.28,-0.9981,-0.060869,0.0096254,259.94,0.060909,-0.99814,0.003952,191.28
> view matrix models
> #3,0.0093669,0.0045308,0.99995,366.49,-0.9981,-0.060869,0.0096254,279.01,0.060909,-0.99814,0.003952,219.33
> view matrix models
> #3,0.0093669,0.0045308,0.99995,290.23,-0.9981,-0.060869,0.0096254,252.39,0.060909,-0.99814,0.003952,179.52
> show #!2 models
> hide #1 models
> view matrix models
> #3,0.0093669,0.0045308,0.99995,289.76,-0.9981,-0.060869,0.0096254,250.4,0.060909,-0.99814,0.003952,179.67
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule AF-P0A6M8-F1-model_v4.pdb (#3) to map
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) using 5453 atoms
average map value = 0.1485, steps = 152
shifted from previous position = 11.9
rotated from previous position = 17.9 degrees
atoms outside contour = 4739, contour level = 0.31892
Position of AF-P0A6M8-F1-model_v4.pdb (#3) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.13778685 0.24209669 0.96041867 287.05182488
-0.96401774 -0.18978973 0.18614427 259.87164913
0.22734251 -0.95150885 0.20723497 187.17214812
Axis -0.62755503 0.40438128 -0.66531982
Axis point 218.35757952 109.32912690 0.00000000
Rotation angle (degrees) 114.98518814
Shift along axis -199.58292457
> hide #!2 models
> select subtract #3
Nothing selected
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #3 models
> save
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/J393_newmask/J393_model_angelo_compare_PDBs.cxs
> includeMaps true
> open 7UG7
Summary of feedback from opening 7UG7 fetched from pdb
---
notes | Fetching compressed mmCIF 7ug7 from http://files.rcsb.org/download/7ug7.cif
Fetching CCD 0UO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/0UO/0UO.cif
Fetching CCD BB9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/BB9/BB9.cif
Fetching CCD DAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DAL/DAL.cif
Fetching CCD DBB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/DBB/DBB.cif
Fetching CCD DHA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/DHA/DHA.cif
Fetching CCD SAR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/SAR/SAR.cif
7ug7 title:
70S ribosome complex in an intermediate state of translocation bound to
EF-G(GDP) stalled by Argyrin B [more info...]
Chain information for 7ug7 #4
---
Chain | Description | UniProt
16 | 16S rRNA |
23 | 23S rRNA |
5 | 5S rRNA |
B | Argyrin B |
Dt | tRNA-fMet |
EF | Elongation factor G | EFG_ECOLI 1-700
LA | 50S ribosomal protein L1 | RL1_ECO45 1-234
LB | 50S ribosomal protein L2 | RL2_ECOLI 1-273
LC | 50S ribosomal protein L3 | RL3_ECOLI 1-209
LD | 50S ribosomal protein L4 | L3C159_ECOLX 1-201
LE | 50S ribosomal protein L5 | A0A829CFT8_ECOLX 1-179
LF | 50S ribosomal protein L6 | A0A862ZNS7_ECOLX 1-177
LI | 50S ribosomal protein L9 | V0YZK9_ECOLX 1-149
LJ | 50S ribosomal protein L10 | RL10_ECOLI 1-165
LK | 50S ribosomal protein L11 | RL11_ECOLI 1-142
LM | 50S ribosomal protein L13 | S1EW51_ECOLX 1-142
LN | 50S ribosomal protein L14 | S1NW45_ECOLX 1-123
LO | 50S ribosomal protein L15 | A0A037Y8L6_ECOLX 1-144
LP | 50S ribosomal protein L16 | RL16_ECOLI 1-136
LQ | 50S ribosomal protein L17 | A0A1X3LC97_ECOLX 1-127
LR | 50S ribosomal protein L18 | L3C145_ECOLX 1-117
LS | 50S ribosomal protein L19 | V0AJX1_ECOLX 1-115
LT | 50S ribosomal protein L20 | RL20_ECO45 1-118
LU | Ribosomal protein L21 | A0A829CSJ4_ECOLX 1-103
LV | 50S ribosomal protein L22 | RL22_ECOLI 1-110
LW | 50S ribosomal protein L23 | A0A829CFV1_ECOLX 1-100
LX | 50S ribosomal protein L24 | A0A1X3KWX7_ECOLX 1-104
LY | 50S ribosomal protein L25 | D7XH79_ECOLX 1-94
La | 50S ribosomal protein L27 | RL27_ECOLI 1-85
Lb | 50S ribosomal protein L28 | A0A1X3JA73_ECOLX 1-78
Lc | 50S ribosomal protein L29 | D6IEL0_ECOLX 1-63
Ld | 50S ribosomal protein L30 | V0YKA9_ECOLX 1-59
Le | 50S ribosomal protein L31 | RL31_ECOLI 1-70
Lf | 50S ribosomal protein L32 | D7XI28_ECOLX 1-57
Lg | 50S ribosomal protein L33 | F4NQ61_ECOLX 1-55
Lh | 50S ribosomal protein L34 | RL34_ECO45 1-46
Li | 50S ribosomal protein L35 | RL35_ECOLI 1-65
Lj | 50S ribosomal protein L36 | A0A0E2L017_ECOU3 1-38
Pt | tRNA-Phe |
SB | 30S ribosomal protein S2 | J7QM75_ECOLX 1-241
SC | 30S ribosomal protein S3 | RS3_ECO45 1-233
SD | 30S ribosomal protein S4 | RS4_ECOLI 1-206
SE | 30S ribosomal protein S5 | RS5_ECOLI 1-167
SF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
SG | 30S ribosomal protein S7 | RS7_ECOLI 1-179
SH | 30S ribosomal protein S8 | D7XKZ3_ECOLX 1-130
SI | 30S ribosomal protein S9 | A0A1Z3UZ18_ECOLX 1-130
SJ | 30S ribosomal protein S10 | V0ANK5_ECOLX 1-103
SK | 30S ribosomal protein S11 | RS11_ECO45 1-129
SL | 30S ribosomal protein S12 | RS12_ECOLI 1-124
SM | 30S ribosomal protein S13 | A0A7U9IV78_ECOLX 1-118
SN | 30S ribosomal protein S14 | U9Y6H3_ECOLX 1-101
SO | 30S ribosomal protein S15 | D8EB41_ECOLX 1-89
SP | 30S ribosomal protein S16 | RS16_ECO45 1-82
SQ | 30S ribosomal protein S17 | A0A829A8C6_ECOLX 1-84
SR | 30S ribosomal protein S18 | A0A0E2KXL3_ECOU3 1-75
SS | 30S ribosomal protein S19 | S1EA57_ECOLX 1-92
ST | 30S ribosomal protein S20 | C3TRH7_ECOLX 1-87
SU | 30S ribosomal protein S21 | A0A0E2L2J1_ECOU3 1-71
mR | mRNA |
Non-standard residues in 7ug7 #4
---
DBB — D-α-aminobutyric acid
FME — N-formylmethionine
GDP — guanosine-5'-diphosphate
MG — magnesium ion
PHE — phenylalanine
PUT — 1,4-diaminobutane (putrescine)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 7PJY
Summary of feedback from opening 7PJY fetched from pdb
---
note | Fetching compressed mmCIF 7pjy from http://files.rcsb.org/download/7pjy.cif
7pjy title:
Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 1
(CHI1-EF-G-GDP) [more info...]
Chain information for 7pjy #5
---
Chain | Description | UniProt
0 | 50S ribosomal protein L32 | RL32_ECOLI 0-56
1 | 50S ribosomal protein L33 | RL33_ECOLI 0-54
2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
3 | 50S ribosomal protein L35 | RL35_ECOLI 0-64
4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
5 | 50S ribosomal protein L10 | RL10_ECOLI 1-165
6 | 50S ribosomal protein L31 | RL31_ECOLI 1-70
A | 23S ribosomal RNA |
B | 5S ribosomal RNA |
C | 50S ribosomal protein L2 | RL2_ECOLI 0-272
D | 50S ribosomal protein L3 | RL3_ECOLI 1-209
E | 50S ribosomal protein L4 | RL4_ECOLI 1-201
F | 50S ribosomal protein L5 | RL5_ECOLI 0-178
G | 50S ribosomal protein L6 | RL6_ECOLI 0-176
H | 50S ribosomal protein L9 | RL9_ECOLI 1-149
I | 50S ribosomal protein L11 | RL11_ECOLI 0-141
J | 50S ribosomal protein L13 | RL13_ECOLI 1-142
K | 50S ribosomal protein L14 | RL14_ECOLI 1-123
L | 50S ribosomal protein L15 | RL15_ECOLI 1-144
M | 50S ribosomal protein L16 | RL16_ECOLI 1-136
N | 50S ribosomal protein L17 | RL17_ECOLI 1-127
O | 50S ribosomal protein L18 | RL18_ECOLI 1-117
P | 50S ribosomal protein L19 | RL19_ECOLI 0-114
Q | 50S ribosomal protein L20 | RL20_ECOLI 0-117
R | 50S ribosomal protein L21 | RL21_ECOLI 1-103
S | 50S ribosomal protein L22 | RL22_ECOLI 1-110
T | 50S ribosomal protein L23 | RL23_ECOLI 1-100
U | 50S ribosomal protein L24 | RL24_ECOLI 0-103
V | 50S ribosomal protein L25 | RL25_ECOLI 1-94
W | 50S ribosomal protein L27 | RL27_ECOLI -3-81
X | 50S ribosomal protein L28 | RL28_ECOLI 0-77
Y | 50S ribosomal protein L29 | RL29_ECOLI 1-63
Z | 50S ribosomal protein L30 | RL30_ECOLI 0-58
a | 16S ribosomal RNA |
b | 30S ribosomal protein S2 | RS2_ECOLI 0-239
c | 30S ribosomal protein S3 | RS3_ECOLI 0-232
d | 30S ribosomal protein S4 | RS4_ECOLI 0-205
e | 30S ribosomal protein S5 | RS5_ECOLI 0-166
f | 30S ribosomal protein S6, fully modified isoform | RS6_ECOLI 1-135
g | 30S ribosomal protein S7 | RS7_ECOLI 0-178
h | 30S ribosomal protein S8 | RS8_ECOLI 0-129
i | 30S ribosomal protein S9 | RS9_ECOLI 0-129
j | 30S ribosomal protein S10 | RS10_ECOLI 1-103
k | 30S ribosomal protein S11 | RS11_ECOLI 0-128
l | 30S ribosomal protein S12 | RS12_ECOLI 0-123
m | 30S ribosomal protein S13 | RS13_ECOLI 0-117
n | 30S ribosomal protein S14 | RS14_ECOLI 0-101
o | 30S ribosomal protein S15 | RS15_ECOLI 0-88
p | 30S ribosomal protein S16 | RS16_ECOLI 1-82
q | 30S ribosomal protein S17 | RS17_ECOLI 0-83
r | 30S ribosomal protein S18 | RS18_ECOLI 0-74
s | 30S ribosomal protein S19 | RS19_ECOLI 0-91
t | 30S ribosomal protein S20 | RS20_ECOLI 0-86
u | 30S ribosomal protein S21 | RS21_ECOLI 0-70
v | P-site tRNA(fMet) |
w | P-site fMet-Phe-tRNA(Phe) |
x | Elongation factor G | EFG_ECOLI 0-703
y | Dipeptide (FME-PHE) |
z | mRNA |
Non-standard residues in 7pjy #5
---
AM2 — apramycin (nebramycin II; 4-O-(3Α-amino-6Α-((4-amino-4-deoxy-α-D-
glucopyranosyl)oxy)-2,3,4,5ABETA,6,7,8,8AALPHA-
octahydro-8Β-hydroxy-7Β-(methylamino)pyrano(3,2-B)pyran-2Α-yl)-2-deoxy-D-
streptamine)
GDP — guanosine-5'-diphosphate
MG — magnesium ion
NA — sodium ion
ZN — zinc ion
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 7PJV
Summary of feedback from opening 7PJV fetched from pdb
---
note | Fetching compressed mmCIF 7pjv from http://files.rcsb.org/download/7pjv.cif
7pjv title:
Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 1
(H1-EF-G-GDP-Pi) [more info...]
Chain information for 7pjv #6
---
Chain | Description | UniProt
0 | 50S ribosomal protein L32 | RL32_ECOLI 0-56
1 | 50S ribosomal protein L33 | RL33_ECOLI 0-54
2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
3 | 50S ribosomal protein L35 | RL35_ECOLI 0-64
4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
5 | 50S ribosomal protein L10 | RL10_ECOLI 1-165
6 | 50S ribosomal protein L31 | RL31_ECOLI 1-70
A | 23S ribosomal RNA |
B | 5S ribosomal RNA |
C | 50S ribosomal protein L2 | RL2_ECOLI 0-272
D | 50S ribosomal protein L3 | RL3_ECOLI 1-209
E | 50S ribosomal protein L4 | RL4_ECOLI 1-201
F | 50S ribosomal protein L5 | RL5_ECOLI 0-178
G | 50S ribosomal protein L6 | RL6_ECOLI 0-176
H | 50S ribosomal protein L9 | RL9_ECOLI 1-149
I | 50S ribosomal protein L11 | RL11_ECOLI 0-141
J | 50S ribosomal protein L13 | RL13_ECOLI 1-142
K | 50S ribosomal protein L14 | RL14_ECOLI 1-123
L | 50S ribosomal protein L15 | RL15_ECOLI 1-144
M | 50S ribosomal protein L16 | RL16_ECOLI 1-136
N | 50S ribosomal protein L17 | RL17_ECOLI 1-127
O | 50S ribosomal protein L18 | RL18_ECOLI 1-117
P | 50S ribosomal protein L19 | RL19_ECOLI 0-114
Q | 50S ribosomal protein L20 | RL20_ECOLI 0-117
R | 50S ribosomal protein L21 | RL21_ECOLI 1-103
S | 50S ribosomal protein L22 | RL22_ECOLI 1-110
T | 50S ribosomal protein L23 | RL23_ECOLI 1-100
U | 50S ribosomal protein L24 | RL24_ECOLI 0-103
V | 50S ribosomal protein L25 | RL25_ECOLI 1-94
W | 50S ribosomal protein L27 | RL27_ECOLI -3-81
X | 50S ribosomal protein L28 | RL28_ECOLI 0-77
Y | 50S ribosomal protein L29 | RL29_ECOLI 1-63
Z | 50S ribosomal protein L30 | RL30_ECOLI 0-58
a | 16S ribosomal RNA |
b | 30S ribosomal protein S2 | RS2_ECOLI 0-239
c | 30S ribosomal protein S3 | RS3_ECOLI 0-232
d | 30S ribosomal protein S4 | RS4_ECOLI 0-205
e | 30S ribosomal protein S5 | RS5_ECOLI 0-166
f | 30S ribosomal protein S6, fully modified isoform | RS6_ECOLI 1-135
g | 30S ribosomal protein S7 | RS7_ECOLI 0-178
h | 30S ribosomal protein S8 | RS8_ECOLI 0-129
i | 30S ribosomal protein S9 | RS9_ECOLI 0-129
j | 30S ribosomal protein S10 | RS10_ECOLI 1-103
k | 30S ribosomal protein S11 | RS11_ECOLI 0-128
l | 30S ribosomal protein S12 | RS12_ECOLI 0-123
m | 30S ribosomal protein S13 | RS13_ECOLI 0-117
n | 30S ribosomal protein S14 | RS14_ECOLI 0-101
o | 30S ribosomal protein S15 | RS15_ECOLI 0-88
p | 30S ribosomal protein S16 | RS16_ECOLI 1-82
q | 30S ribosomal protein S17 | RS17_ECOLI 0-83
r | 30S ribosomal protein S18 | A0A6D2XHZ3_ECOLI 0-74
s | 30S ribosomal protein S19 | RS19_ECOLI 0-91
t | 30S ribosomal protein S20 | RS20_ECOLI 0-86
u | 30S ribosomal protein S21 | RS21_ECOLI 0-70
v | P-site tRNA(fMet) |
w | P-site fMet-Phe-tRNA(Phe) |
x | Elongation factor G | EFG_ECOLI 0-703
y | Dipeptide (FME-PHE) |
z | mRNA |
Non-standard residues in 7pjv #6
---
AM2 — apramycin (nebramycin II; 4-O-(3Α-amino-6Α-((4-amino-4-deoxy-α-D-
glucopyranosyl)oxy)-2,3,4,5ABETA,6,7,8,8AALPHA-
octahydro-8Β-hydroxy-7Β-(methylamino)pyrano(3,2-B)pyran-2Α-yl)-2-deoxy-D-
streptamine)
GDP — guanosine-5'-diphosphate
MG — magnesium ion
NA — sodium ion
PO4 — phosphate ion
ZN — zinc ion
> open 7N2C
7n2c title:
Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state
of translocation bound to EF-G(GDP) (INT2) [more info...]
Chain information for 7n2c #7
---
Chain | Description | UniProt
16 | 16S rRNA |
23 | 23S rRNA |
5 | 5S rRNA |
Dt | tRNA |
EF | Elongation factor G | EFG_ECOLI 1-704
LA | 50S ribosomal protein L1 | A0A4S5ALA4_ECOLI 1-234
LB | 50S ribosomal protein L2 | RL2_ECOLI 1-273
LC | 50S ribosomal protein L3 | RL3_ECOLI 1-209
LD | 50S ribosomal protein L4 | RL4_ECOLI 1-201
LE | 50S ribosomal protein L5 | RL5_ECOLI 1-179
LF | 50S ribosomal protein L6 | RL6_ECOLI 1-177
LG | 50S ribosomal protein L7/L12 | RL7_ECOLI 0-120
LI | 50S ribosomal protein L9 | RL9_ECOLI 1-149
LJ | 50S ribosomal protein L10 | RL10_ECOLI 1-165
LK | 50S ribosomal protein L11 | RL11_ECOLI 1-142
LM | 50S ribosomal protein L13 | RL13_ECOLI 1-142
LN | 50S ribosomal protein L14 | RL14_ECOLI 1-123
LO | 50S ribosomal protein L15 | RL15_ECOLI 1-144
LP | 50S ribosomal protein L16 | RL16_ECOLI 1-136
LQ | 50S ribosomal protein L17 | RL17_ECOLI 1-127
LR | 50S ribosomal protein L18 | RL18_ECOLI 1-117
LS | 50S ribosomal protein L19 | RL19_ECOLI 1-115
LT | 50S ribosomal protein L20 | RL20_ECOLI 1-118
LU | 50S ribosomal protein L21 | RL21_ECOLI 1-103
LV | 50S ribosomal protein L22 | RL22_ECOLI 1-110
LW | 50S ribosomal protein L23 | RL23_ECOLI 1-100
LX | 50S ribosomal protein L24 | RL24_ECOLI 1-104
LY | 50S ribosomal protein L25 | RL25_ECOLI 1-94
La | 50S ribosomal protein L27 | RL27_ECOLI 1-85
Lb | 50S ribosomal protein L28 | RL28_ECOLI 1-78
Lc | 50S ribosomal protein L29 | RL29_ECOLI 1-63
Ld | 50S ribosomal protein L30 | RL30_ECOLI 1-59
Le | 50S ribosomal protein L31 | RL31_ECOLI 1-70
Lf | 50S ribosomal protein L32 | RL32_ECOLI 1-57
Lg | 50S ribosomal protein L33 | RL33_ECOLI 1-55
Lh | 50S ribosomal protein L34 | RL34_ECOLI 1-46
Li | 50S ribosomal protein L35 | RL35_ECOLI 1-65
Lj | 50S ribosomal protein L36 | RL36_ECOLI 1-38
Pp | Polypeptide |
Pt | Chains: Pt |
SB | 30S ribosomal protein S2 | RS2_ECOLI 1-241
SC | 30S ribosomal protein S3 | RS3_ECOLI 1-233
SD | 30S ribosomal protein S4 | RS4_ECOLI 1-206
SE | 30S ribosomal protein S5 | RS5_ECOLI 1-167
SF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
SG | 30S ribosomal protein S7 | RS7_ECOLI 1-179
SH | 30S ribosomal protein S8 | RS8_ECOLI 1-130
SI | 30S ribosomal protein S9 | RS9_ECOLI 1-130
SJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
SK | 30S ribosomal protein S11 | RS11_ECOLI 1-129
SL | 30S ribosomal protein S12 | A0A4S5B3M5_ECOLI 1-124
SM | 30S ribosomal protein S13 | RS13_ECOLI 1-118
SN | 30S ribosomal protein S14 | RS14_ECOLI 1-101
SO | 30S ribosomal protein S15 | RS15_ECOLI 1-89
SP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
SQ | 30S ribosomal protein S17 | RS17_ECOLI 1-84
SR | 30S ribosomal protein S18 | RS18_ECOLI 1-75
SS | 30S ribosomal protein S19 | RS19_ECOLI 1-92
ST | 30S ribosomal protein S20 | RS20_ECOLI 1-87
SU | 30S ribosomal protein S21 | RS21_ECOLI 1-71
mR | Chains: mR |
Non-standard residues in 7n2c #7
---
ATP — adenosine-5'-triphosphate
FUA — fusidic acid
GDP — guanosine-5'-diphosphate
MG — magnesium ion
PUT — 1,4-diaminobutane (putrescine)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #1 models
> select add #4
154323 atoms, 166742 bonds, 5430 pseudobonds, 11906 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,168.11,0,1,0,-40.498,0,0,1,-106.76
> view matrix models #4,1,0,0,177.48,0,1,0,-5.7915,0,0,1,-155.64
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.86895,0.49478,0.01046,424.83,0.26632,0.48532,-0.83279,229.82,-0.41713,-0.72087,-0.55349,406.5
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.86895,0.49478,0.01046,365.55,0.26632,0.48532,-0.83279,252.89,-0.41713,-0.72087,-0.55349,579.48
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.9851,-0.023043,-0.17042,533.07,0.11891,0.62459,-0.77184,238.78,0.12423,-0.78061,-0.61255,502.71
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.9851,-0.023043,-0.17042,506.11,0.11891,0.62459,-0.77184,237.97,0.12423,-0.78061,-0.61255,465.96
> view matrix models
> #4,-0.9851,-0.023043,-0.17042,467.39,0.11891,0.62459,-0.77184,229.1,0.12423,-0.78061,-0.61255,490.86
> view matrix models
> #4,-0.9851,-0.023043,-0.17042,470.18,0.11891,0.62459,-0.77184,230.69,0.12423,-0.78061,-0.61255,494.12
> fitmap #4 inMap #2
Fit molecule 7ug7 (#4) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 154323 atoms
average map value = 0.564, steps = 416
shifted from previous position = 6.47
rotated from previous position = 24 degrees
atoms outside contour = 55226, contour level = 0.31892
Position of 7ug7 (#4) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.87343684 0.22632921 -0.43114169 445.65804540
0.48662192 0.43758031 -0.75612338 197.80088261
0.01752631 -0.87022902 -0.49233552 506.78617184
Axis -0.21484464 -0.84477784 0.49009405
Axis point 156.55420507 0.00000000 346.18401818
Rotation angle (degrees) 164.60013512
Shift along axis -14.47215831
> select subtract #4
Nothing selected
> select #4/EF
5208 atoms, 5307 bonds, 2 pseudobonds, 674 residues, 3 models selected
> fitmap sel inMap #2
Fit molecule 7ug7 (#4) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5208 atoms
average map value = 0.1644, steps = 144
shifted from previous position = 7.06
rotated from previous position = 9.57 degrees
atoms outside contour = 4372, contour level = 0.31892
Position of 7ug7 (#4) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.93076031 0.09756483 -0.35237244 473.98597496
0.35223176 0.49776384 -0.79256794 215.44418647
0.09807150 -0.86180755 -0.49766426 488.05745717
Axis -0.13262708 -0.86281635 0.48780940
Axis point 182.46919224 0.00000000 341.30408909
Rotation angle (degrees) 164.86874236
Shift along axis -10.67312906
> select add #4
154323 atoms, 166742 bonds, 5430 pseudobonds, 11906 residues, 4 models
selected
> select subtract #4
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> select #4
154323 atoms, 166742 bonds, 5430 pseudobonds, 11906 residues, 4 models
selected
> hide sel atoms
> hide sel cartoons
> select #4/EF
5208 atoms, 5307 bonds, 2 pseudobonds, 674 residues, 3 models selected
> show sel cartoons
> select add #4
154323 atoms, 166742 bonds, 5430 pseudobonds, 11906 residues, 4 models
selected
> select subtract #4
Nothing selected
> hide #!2 models
> show #1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!2 models
> hide #1 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #5
153084 atoms, 165637 bonds, 5216 pseudobonds, 11703 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.86204,0.45931,0.21429,-88.818,-0.48745,0.86714,0.10228,89.821,-0.13884,-0.19263,0.9714,61.167
> view matrix models
> #5,-0.67642,0.030756,0.73587,162.06,-0.70844,-0.3004,-0.63865,449.4,0.20141,-0.95332,0.22499,255.94
> view matrix models
> #5,0.098316,-0.1448,-0.98457,351,-0.89142,-0.45262,-0.02245,400.85,-0.44238,0.87987,-0.17357,133.11
> view matrix models
> #5,0.75225,-0.65695,-0.050359,160.98,0.075938,0.16237,-0.9838,294.59,0.65449,0.73624,0.17203,-94.492
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.75225,-0.65695,-0.050359,230.17,0.075938,0.16237,-0.9838,349.39,0.65449,0.73624,0.17203,-75.181
> view matrix models
> #5,0.75225,-0.65695,-0.050359,209.37,0.075938,0.16237,-0.9838,375.75,0.65449,0.73624,0.17203,-50.341
> view matrix models
> #5,0.75225,-0.65695,-0.050359,213.21,0.075938,0.16237,-0.9838,378.06,0.65449,0.73624,0.17203,-26.929
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.63407,-0.76549,0.10945,224.45,0.073755,-0.081021,-0.99398,420.55,0.76975,0.63833,0.0050855,-2.2005
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.63407,-0.76549,0.10945,220.62,0.073755,-0.081021,-0.99398,405.95,0.76975,0.63833,0.0050855,-9.5577
> view matrix models
> #5,0.63407,-0.76549,0.10945,211.46,0.073755,-0.081021,-0.99398,409.91,0.76975,0.63833,0.0050855,-11.461
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.7696,-0.63141,0.095039,167.97,0.060354,-0.076241,-0.99526,411.68,0.63567,0.77169,-0.020567,-5.6936
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.7696,-0.63141,0.095039,174.42,0.060354,-0.076241,-0.99526,410.51,0.63567,0.77169,-0.020567,-4.4722
> view matrix models
> #5,0.7696,-0.63141,0.095039,174.26,0.060354,-0.076241,-0.99526,410.15,0.63567,0.77169,-0.020567,-2.5379
> fitmap #5 inMap #2
Fit molecule 7pjy (#5) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153084 atoms
average map value = 0.1426, steps = 88
shifted from previous position = 5.26
rotated from previous position = 4.7 degrees
atoms outside contour = 125790, contour level = 0.31892
Position of 7pjy (#5) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.81622435 -0.57469119 0.05922719 168.16282861
0.02867258 -0.06209466 -0.99765833 411.85212139
0.57702314 0.81601121 -0.03420530 3.03216754
Axis 0.91585950 -0.26147450 0.30468419
Axis point 0.00000000 235.31916855 174.68423448
Rotation angle (degrees) 98.05003381
Shift along axis 47.24854851
> view matrix models
> #5,0.81622,-0.57469,0.059227,164.38,0.028673,-0.062095,-0.99766,411.24,0.57702,0.81601,-0.034205,2.6929
> fitmap #5 inMap #2
Fit molecule 7pjy (#5) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153084 atoms
average map value = 0.5201, steps = 324
shifted from previous position = 17.9
rotated from previous position = 19.1 degrees
atoms outside contour = 61222, contour level = 0.31892
Position of 7pjy (#5) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.94102447 -0.32546458 -0.09244331 143.89045466
-0.12746553 -0.08793590 -0.98793715 434.22054032
0.31340946 0.94145637 -0.12423535 48.52365243
Axis 0.97368651 -0.20481740 0.09992207
Axis point 0.00000000 213.01183510 216.56291092
Rotation angle (degrees) 97.79177758
Shift along axis 56.01685574
> select subtract #5
Nothing selected
> select #5/x
5433 atoms, 5535 bonds, 1 pseudobond, 698 residues, 2 models selected
> fitmap #5 inMap #2
Fit molecule 7pjy (#5) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153084 atoms
average map value = 0.5201, steps = 60
shifted from previous position = 0.0141
rotated from previous position = 0.00259 degrees
atoms outside contour = 61189, contour level = 0.31892
Position of 7pjy (#5) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.94103776 -0.32542300 -0.09245440 143.87747694
-0.12747200 -0.08793764 -0.98793616 434.21876839
0.31336692 0.94147058 -0.12423497 48.51595272
Axis 0.97369238 -0.20480136 0.09989774
Axis point 0.00000000 213.01085916 216.55979360
Rotation angle (degrees) 97.79143270
Shift along axis 56.01044010
> fitmap sel inMap #2
Fit molecule 7pjy (#5) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5433 atoms
average map value = 0.1573, steps = 108
shifted from previous position = 7.36
rotated from previous position = 8.11 degrees
atoms outside contour = 4590, contour level = 0.31892
Position of 7pjy (#5) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.96521625 -0.25969855 0.03023678 113.10841784
-0.00087290 -0.11884936 -0.99291191 417.55519605
0.26145141 0.95834832 -0.11494203 50.53413766
Axis 0.98454775 -0.11666401 0.13059571
Axis point 0.00000000 197.07081742 206.60565265
Rotation angle (degrees) 97.71742570
Shift along axis 69.24651743
> select add #5
153084 atoms, 165637 bonds, 5216 pseudobonds, 11703 residues, 4 models
selected
> select subtract #5
Nothing selected
> select #5
153084 atoms, 165637 bonds, 5216 pseudobonds, 11703 residues, 4 models
selected
> hide sel atoms
> select #5/x
5433 atoms, 5535 bonds, 1 pseudobond, 698 residues, 2 models selected
> show sel cartoons
> select add #5
153084 atoms, 165637 bonds, 5216 pseudobonds, 11703 residues, 4 models
selected
> select subtract #5
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> hide #!5 models
> show #1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> open /home/miramay/Downloads/cryosparc_P249_cryosparc_P249_J412_mask.mrc
Opened cryosparc_P249_cryosparc_P249_J412_mask.mrc as #8, grid size
440,440,440, pixel 1.06, shown at level 5e-05, step 2, values float32
> color #8 #d4d4d4dc models
> hide #!8 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!2 models
> select add #6
153165 atoms, 165666 bonds, 5263 pseudobonds, 11762 residues, 3 models
selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,65.266,0,1,0,71.671,0,0,1,243.38
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99484,-0.10142,-0.0018331,83.135,-0.020322,-0.18157,-0.98317,439.95,0.099379,0.97813,-0.1827,270.83
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.99484,-0.10142,-0.0018331,35.735,-0.020322,-0.18157,-0.98317,451.78,0.099379,0.97813,-0.1827,98.858
> view matrix models
> #6,0.99484,-0.10142,-0.0018331,90.572,-0.020322,-0.18157,-0.98317,427.48,0.099379,0.97813,-0.1827,71.296
> view matrix models
> #6,0.99484,-0.10142,-0.0018331,93.931,-0.020322,-0.18157,-0.98317,430.09,0.099379,0.97813,-0.1827,77.352
> ui tool show "Fit in Map"
> fitmap #6 inMap #2
Fit molecule 7pjv (#6) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153165 atoms
average map value = 0.259, steps = 320
shifted from previous position = 11
rotated from previous position = 12.7 degrees
atoms outside contour = 102922, contour level = 0.31892
Position of 7pjv (#6) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.95110176 -0.29677432 0.08561797 112.11805798
0.01954597 -0.21880706 -0.97557236 429.44602831
0.30825864 0.92954207 -0.20230704 62.40195687
Axis 0.98000331 -0.11452782 0.16271722
Axis point 0.00000000 200.84600312 197.59414703
Rotation angle (degrees) 103.59198638
Shift along axis 70.84642533
> fitmap #6 inMap #2
Fit molecule 7pjv (#6) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153165 atoms
average map value = 0.259, steps = 148
shifted from previous position = 0.00326
rotated from previous position = 0.000984 degrees
atoms outside contour = 102932, contour level = 0.31892
Position of 7pjv (#6) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.95110438 -0.29677055 0.08560203 112.11808228
0.01953054 -0.21880685 -0.97557272 429.45146930
0.30825156 0.92954333 -0.20231207 62.40409400
Axis 0.98000441 -0.11453240 0.16270739
Axis point 0.00000000 200.84771166 197.59757545
Rotation angle (degrees) 103.59205138
Shift along axis 70.84371291
> select #6/x
5478 atoms, 5580 bonds, 4 pseudobonds, 706 residues, 2 models selected
> fitmap #6 inMap #2
Fit molecule 7pjv (#6) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153165 atoms
average map value = 0.259, steps = 360
shifted from previous position = 0.00794
rotated from previous position = 0.00889 degrees
atoms outside contour = 102931, contour level = 0.31892
Position of 7pjv (#6) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.95112508 -0.29668402 0.08567187 112.09354879
0.01964566 -0.21873391 -0.97558676 429.42895318
0.30818034 0.92958812 -0.20221475 62.39127069
Axis 0.98001140 -0.11445713 0.16271823
Axis point 0.00000000 200.83487631 197.59843661
Rotation angle (degrees) 103.58642319
Shift along axis 70.85394945
> fitmap sel inMap #2
Fit molecule 7pjv (#6) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5478 atoms
average map value = 0.149, steps = 232
shifted from previous position = 12.3
rotated from previous position = 19.7 degrees
atoms outside contour = 4761, contour level = 0.31892
Position of 7pjv (#6) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.99545218 -0.08084941 -0.05038181 99.10920621
-0.04883236 0.02103011 -0.99858557 411.21728891
0.08179459 0.99650444 0.01698640 68.03351240
Axis 0.99768471 -0.06609745 0.01601076
Axis point 0.00000000 174.81446657 245.23720247
Rotation angle (degrees) 89.04114766
Shift along axis 72.78859206
> select #6
153165 atoms, 165666 bonds, 5263 pseudobonds, 11762 residues, 3 models
selected
> hide sel atoms
> select #6/xx
Nothing selected
> show #1#!6 cartoons
> hide #1 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> close #6
> show #!7 models
> select add #7
155157 atoms, 167836 bonds, 5164 pseudobonds, 11828 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.36637,-0.89141,0.26677,372.19,0.263,-0.17581,-0.94864,572.94,0.89253,0.41771,0.17003,-129.96
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.36637,-0.89141,0.26677,335.34,0.263,-0.17581,-0.94864,502.98,0.89253,0.41771,0.17003,-215.69
> view matrix models
> #7,0.36637,-0.89141,0.26677,332.61,0.263,-0.17581,-0.94864,503.96,0.89253,0.41771,0.17003,-217.06
> fitmap #7 inMap #2
Fit molecule 7n2c (#7) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 155157 atoms
average map value = 0.5283, steps = 256
shifted from previous position = 18
rotated from previous position = 14.1 degrees
atoms outside contour = 62410, contour level = 0.31892
Position of 7n2c (#7) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.12841303 -0.95135192 0.28007070 401.58683229
0.28656396 -0.23476658 -0.92885182 505.35559412
0.94941621 0.19953484 0.24247609 -191.44220196
Axis 0.62555882 -0.37107403 0.68627999
Axis point 67.67151057 404.63469054 0.00000000
Rotation angle (degrees) 115.59066055
Shift along axis -67.69110785
> select subtract #7
Nothing selected
> select add #7
155157 atoms, 167836 bonds, 5164 pseudobonds, 11828 residues, 4 models
selected
> select #7/EF
5065 atoms, 5167 bonds, 4 pseudobonds, 688 residues, 3 models selected
> fitmap sel inMap #2
Fit molecule 7n2c (#7) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5065 atoms
average map value = 0.1643, steps = 136
shifted from previous position = 7.42
rotated from previous position = 8.43 degrees
atoms outside contour = 4226, contour level = 0.31892
Position of 7n2c (#7) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.15645386 -0.89753746 0.41224831 339.38208116
0.28501911 -0.35860423 -0.88891342 529.94829966
0.94566709 0.25657259 0.19971031 -195.88085963
Axis 0.66188589 -0.30822058 0.68330604
Axis point 50.47140776 384.19618676 -0.00000000
Rotation angle (degrees) 120.08074954
Shift along axis -72.55533585
> select add #7
155157 atoms, 167836 bonds, 5164 pseudobonds, 11828 residues, 4 models
selected
> select subtract #7
Nothing selected
> select #7/EF
5065 atoms, 5167 bonds, 4 pseudobonds, 688 residues, 3 models selected
> show sel cartoons
> select #7
155157 atoms, 167836 bonds, 5164 pseudobonds, 11828 residues, 4 models
selected
> hide sel atoms
> close #8
> open 7pjv
7pjv title:
Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 1
(H1-EF-G-GDP-Pi) [more info...]
Chain information for 7pjv #6
---
Chain | Description | UniProt
0 | 50S ribosomal protein L32 | RL32_ECOLI 0-56
1 | 50S ribosomal protein L33 | RL33_ECOLI 0-54
2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
3 | 50S ribosomal protein L35 | RL35_ECOLI 0-64
4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
5 | 50S ribosomal protein L10 | RL10_ECOLI 1-165
6 | 50S ribosomal protein L31 | RL31_ECOLI 1-70
A | 23S ribosomal RNA |
B | 5S ribosomal RNA |
C | 50S ribosomal protein L2 | RL2_ECOLI 0-272
D | 50S ribosomal protein L3 | RL3_ECOLI 1-209
E | 50S ribosomal protein L4 | RL4_ECOLI 1-201
F | 50S ribosomal protein L5 | RL5_ECOLI 0-178
G | 50S ribosomal protein L6 | RL6_ECOLI 0-176
H | 50S ribosomal protein L9 | RL9_ECOLI 1-149
I | 50S ribosomal protein L11 | RL11_ECOLI 0-141
J | 50S ribosomal protein L13 | RL13_ECOLI 1-142
K | 50S ribosomal protein L14 | RL14_ECOLI 1-123
L | 50S ribosomal protein L15 | RL15_ECOLI 1-144
M | 50S ribosomal protein L16 | RL16_ECOLI 1-136
N | 50S ribosomal protein L17 | RL17_ECOLI 1-127
O | 50S ribosomal protein L18 | RL18_ECOLI 1-117
P | 50S ribosomal protein L19 | RL19_ECOLI 0-114
Q | 50S ribosomal protein L20 | RL20_ECOLI 0-117
R | 50S ribosomal protein L21 | RL21_ECOLI 1-103
S | 50S ribosomal protein L22 | RL22_ECOLI 1-110
T | 50S ribosomal protein L23 | RL23_ECOLI 1-100
U | 50S ribosomal protein L24 | RL24_ECOLI 0-103
V | 50S ribosomal protein L25 | RL25_ECOLI 1-94
W | 50S ribosomal protein L27 | RL27_ECOLI -3-81
X | 50S ribosomal protein L28 | RL28_ECOLI 0-77
Y | 50S ribosomal protein L29 | RL29_ECOLI 1-63
Z | 50S ribosomal protein L30 | RL30_ECOLI 0-58
a | 16S ribosomal RNA |
b | 30S ribosomal protein S2 | RS2_ECOLI 0-239
c | 30S ribosomal protein S3 | RS3_ECOLI 0-232
d | 30S ribosomal protein S4 | RS4_ECOLI 0-205
e | 30S ribosomal protein S5 | RS5_ECOLI 0-166
f | 30S ribosomal protein S6, fully modified isoform | RS6_ECOLI 1-135
g | 30S ribosomal protein S7 | RS7_ECOLI 0-178
h | 30S ribosomal protein S8 | RS8_ECOLI 0-129
i | 30S ribosomal protein S9 | RS9_ECOLI 0-129
j | 30S ribosomal protein S10 | RS10_ECOLI 1-103
k | 30S ribosomal protein S11 | RS11_ECOLI 0-128
l | 30S ribosomal protein S12 | RS12_ECOLI 0-123
m | 30S ribosomal protein S13 | RS13_ECOLI 0-117
n | 30S ribosomal protein S14 | RS14_ECOLI 0-101
o | 30S ribosomal protein S15 | RS15_ECOLI 0-88
p | 30S ribosomal protein S16 | RS16_ECOLI 1-82
q | 30S ribosomal protein S17 | RS17_ECOLI 0-83
r | 30S ribosomal protein S18 | A0A6D2XHZ3_ECOLI 0-74
s | 30S ribosomal protein S19 | RS19_ECOLI 0-91
t | 30S ribosomal protein S20 | RS20_ECOLI 0-86
u | 30S ribosomal protein S21 | RS21_ECOLI 0-70
v | P-site tRNA(fMet) |
w | P-site fMet-Phe-tRNA(Phe) |
x | Elongation factor G | EFG_ECOLI 0-703
y | Dipeptide (FME-PHE) |
z | mRNA |
Non-standard residues in 7pjv #6
---
AM2 — apramycin (nebramycin II; 4-O-(3Α-amino-6Α-((4-amino-4-deoxy-α-D-
glucopyranosyl)oxy)-2,3,4,5ABETA,6,7,8,8AALPHA-
octahydro-8Β-hydroxy-7Β-(methylamino)pyrano(3,2-B)pyran-2Α-yl)-2-deoxy-D-
streptamine)
GDP — guanosine-5'-diphosphate
MG — magnesium ion
NA — sodium ion
PO4 — phosphate ion
ZN — zinc ion
> select add #6
308322 atoms, 333502 bonds, 10427 pseudobonds, 23590 residues, 7 models
selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.15645,-0.89754,0.41225,449.73,0.28502,-0.3586,-0.88891,693.05,0.94567,0.25657,0.19971,-141.62,#6,1,0,0,110.35,0,1,0,163.1,0,0,1,54.258
> undo
> select subtract #7
153165 atoms, 165666 bonds, 5263 pseudobonds, 11762 residues, 3 models
selected
> view matrix models #6,1,0,0,10.322,0,1,0,52.804,0,0,1,-29.313
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.88644,-0.44184,-0.13787,126.44,-0.16231,-0.017789,-0.98658,419.28,0.43346,0.89692,-0.087485,-62.691
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.88644,-0.44184,-0.13787,184.49,-0.16231,-0.017789,-0.98658,429.34,0.43346,0.89692,-0.087485,35.211
> view matrix models
> #6,0.88644,-0.44184,-0.13787,185.45,-0.16231,-0.017789,-0.98658,431.16,0.43346,0.89692,-0.087485,35.688
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.97236,-0.2322,0.024491,107.99,-0.015293,-0.16801,-0.98567,430.31,0.23298,0.95805,-0.16692,74.028
> fitmap sel inMap #2
Fit molecule 7pjv (#6) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153165 atoms
average map value = 0.4838, steps = 200
shifted from previous position = 8.64
rotated from previous position = 10.2 degrees
atoms outside contour = 68078, contour level = 0.31892
Position of 7pjv (#6) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.92817460 -0.36616448 -0.06644906 148.36578463
-0.10219311 -0.07909324 -0.99161526 428.99003837
0.35783861 0.92718274 -0.11083182 41.39762042
Axis 0.96772253 -0.21398435 0.13313076
Axis point 0.00000000 215.60205591 210.35850682
Rotation angle (degrees) 97.52017144
Shift along axis 57.29105459
> select #6/x
5478 atoms, 5580 bonds, 4 pseudobonds, 706 residues, 2 models selected
> fitmap sel inMap #2
Fit molecule 7pjv (#6) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5478 atoms
average map value = 0.1457, steps = 92
shifted from previous position = 10.3
rotated from previous position = 8.14 degrees
atoms outside contour = 4768, contour level = 0.31892
Position of 7pjv (#6) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.95926211 -0.25654784 -0.11831905 132.75327549
-0.12296533 -0.00208581 -0.99240877 429.71406666
0.25435354 0.96652928 -0.03354733 39.96167386
Axis 0.98018391 -0.18647230 0.06684001
Axis point 0.00000000 209.59228141 231.26052232
Rotation angle (degrees) 92.18840100
Shift along axis 52.66389342
> hide #!7 models
> show sel cartoons
> select #6
153165 atoms, 165666 bonds, 5263 pseudobonds, 11762 residues, 3 models
selected
> hide sel atoms
> select subtract #6
Nothing selected
> hide #!2 models
> show #1 models
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W
3936 atoms, 4295 bonds, 256 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W
3936 atoms, 4295 bonds, 256 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, BV,.
> Bs, BO
Expected an objects specifier or a keyword
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, BV,
> Bs, BO
4205 atoms, 4592 bonds, 269 residues, 1 model selected
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, Bv,
> Bs, BO
4441 atoms, 4856 bonds, 280 residues, 1 model selected
> hide sel cartoons
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, Bv,
> Bs, BO, J, G, AN
4801 atoms, 5219 bonds, 327 residues, 1 model selected
> hide sel cartoons
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, Bv,
> Bs, BO, J, G, An
4979 atoms, 5399 bonds, 350 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> save
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J393_big_mask/EFG_PDBs_compare.cxs
> includeMaps true
> open 4V9P
Summary of feedback from opening 4V9P fetched from pdb
---
note | Fetching compressed mmCIF 4v9p from http://files.rcsb.org/download/4v9p.cif
4v9p title:
Control of ribosomal subunit rotation by elongation factor G [more info...]
Chain information for 4v9p #8
---
Chain | Description | UniProt
A0 C0 E0 G0 | 50S ribosomal protein L32 | RL32_ECOLI 0-56
A1 C1 E1 G1 | 50S ribosomal protein L33 | RL33_ECOLI 0-54
A2 C2 E2 G2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
A3 C3 E3 G3 | 50S ribosomal protein L35 | RL35_ECOLI 0-64
A4 C4 E4 G4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
A5 E5 | 50S ribosomal protein L10 | RL10_ECOLI 1-165
AA CA EA GA | 23S rRNA |
AB CB EB GB | 5S rRNA |
AC CC EC GC | 50S ribosomal protein L2 | RL2_ECOLI 0-272
AD CD ED GD | 50S ribosomal protein L3 | RL3_ECOLI 1-209
AE CE EE GE | 50S ribosomal protein L4 | RL4_ECOLI 1-201
AF CF EF GF | 50S ribosomal protein L5 | RL5_ECOLI 0-178
AG CG EG GG | 50S ribosomal protein L6 | RL6_ECOLI 0-176
AH CH EH GH | 50S ribosomal protein L9 | RL9_ECOLI 1-50
AI CI EI GI | 50S ribosomal protein L11 | RL11_ECOLI 0-141
AJ CJ EJ GJ | 50S ribosomal protein L13 | RL13_ECOLI 1-142
AK CK EK GK | 50S ribosomal protein L14 | RL14_ECOLI 1-123
AL CL EL GL | 50S ribosomal protein L15 | RL15_ECOLI 1-144
AM CM EM GM | 50S ribosomal protein L16 | RL16_ECOLI 1-136
AN CN EN GN | 50S ribosomal protein L17 | RL17_ECOLI 1-127
AO CO EO GO | 50S ribosomal protein L18 | RL18_ECOLI 1-117
AP CP EP GP | 50S ribosomal protein L19 | RL19_ECOLI 0-114
AQ CQ EQ GQ | 50S ribosomal protein L20 | RL20_ECOLI 0-117
AR CR ER GR | 50S ribosomal protein L21 | RL21_ECOLI 1-103
AS CS ES GS | 50S ribosomal protein L22 | RL22_ECOLI 1-110
AT CT ET GT | 50S ribosomal protein L23 | RL23_ECOLI 1-100
AU CU EU GU | 50S ribosomal protein L24 | RL24_ECOLI 0-103
AV CV EV GV | 50S ribosomal protein L25 | RL25_ECOLI 1-94
AW CW EW GW | 50S ribosomal protein L27 | RL27_ECOLI 0-84
AX CX EX GX | 50S ribosomal protein L28 | RL28_ECOLI 0-77
AY CY EY GY | 50S ribosomal protein L29 | RL29_ECOLI 1-63
AZ CZ EZ GZ | 50S ribosomal protein L30 | RL30_ECOLI 0-58
BA DA FA HA | 16S rRNA |
BB DB FB HB | 30S ribosomal protein S2 | RS2_ECOLI 0-240
BC DC FC HC | 30S ribosomal protein S3 | RS3_ECOLI 1-233
BD DD FD HD | 30S ribosomal protein S4 | RS4_ECOLI 1-206
BE DE FE HE | 30S ribosomal protein S5 | RS5_ECOLI 1-167
BF DF FF HF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
BG DG FG HG | 30S ribosomal protein S7 | RS7_ECOLI 1-179
BH DH FH HH | 30S ribosomal protein S8 | RS8_ECOLI 1-130
BI DI FI HI | 30S ribosomal protein S9 | RS9_ECOLI 1-130
BJ DJ FJ HJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
BK DK FK HK | 30S ribosomal protein S11 | RS11_ECOLI 1-129
BL DL FL HL | 30S ribosomal protein S12 | RS12_ECOLI 1-124
BM DM FM HM | 30S ribosomal protein S13 | RS13_ECOLI 1-118
BN DN FN HN | 30S ribosomal protein S14 | RS14_ECOLI 1-101
BO DO FO HO | 30S ribosomal protein S15 | RS15_ECOLI 1-89
BP DP FP HP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
BQ DQ FQ HQ | 30S ribosomal protein S17 | RS17_ECOLI 1-84
BR DR FR HR | 30S ribosomal protein S18 | RS18_ECOLI 1-75
BS DS FS HS | 30S ribosomal protein S19 | RS19_ECOLI 1-92
BT DT FT HT | 30S ribosomal protein S20 | RS20_ECOLI 1-87
BU DU FU HU | 30S ribosomal protein S21 | RS21_ECOLI 1-71
BV DV FV HV | elongation factor G | EFG_ECOLI 1-704
BW DW FW | Viomycin |
Non-standard residues in 4v9p #8
---
GCP — phosphomethylphosphonic acid guanylate ester
MG — magnesium ion
UAL — (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
ZN — zinc ion
4v9p mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> open 4V9O
Summary of feedback from opening 4V9O fetched from pdb
---
note | Fetching compressed mmCIF 4v9o from http://files.rcsb.org/download/4v9o.cif
4v9o title:
Control of ribosomal subunit rotation by elongation factor G [more info...]
Chain information for 4v9o #9
---
Chain | Description | UniProt
A0 C0 E0 G0 | 50S ribosomal protein L32 | RL32_ECOLI 0-56
A1 C1 E1 G1 | 50S ribosomal protein L33 | RL33_ECOLI 0-54
A2 C2 E2 G2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
A3 C3 E3 G3 | 50S ribosomal protein L35 | RL35_ECOLI 0-64
A4 C4 E4 G4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
A5 C5 E5 | 50S ribosomal protein L10 | RL10_ECOLI 1-165
A6 | 50S ribosomal protein L7/L12 | RL7_ECOLI 0-120
AA CA EA GA | 23S rRNA |
AB CB EB GB | 5S rRNA |
AC CC EC GC | 50S ribosomal protein L2 | RL2_ECOLI 0-272
AD CD ED GD | 50S ribosomal protein L3 | RL3_ECOLI 1-209
AE CE EE GE | 50S ribosomal protein L4 | RL4_ECOLI 1-201
AF CF EF GF | 50S ribosomal protein L5 | RL5_ECOLI 0-178
AG CG EG GG | 50S ribosomal protein L6 | RL6_ECOLI 0-176
AH CH EH GH | 50S ribosomal protein L9 | RL9_ECOLI 1-50
AI CI EI GI | 50S ribosomal protein L11 | RL11_ECOLI 0-141
AJ CJ EJ GJ | 50S ribosomal protein L13 | RL13_ECOLI 1-142
AK CK EK GK | 50S ribosomal protein L14 | RL14_ECOLI 1-123
AL CL EL GL | 50S ribosomal protein L15 | RL15_ECOLI 1-144
AM CM EM GM | 50S ribosomal protein L16 | RL16_ECOLI 1-136
AN CN EN GN | 50S ribosomal protein L17 | RL17_ECOLI 1-127
AO CO EO GO | 50S ribosomal protein L18 | RL18_ECOLI 1-117
AP CP EP GP | 50S ribosomal protein L19 | RL19_ECOLI 0-114
AQ CQ EQ GQ | 50S ribosomal protein L20 | RL20_ECOLI 0-117
AR CR ER GR | 50S ribosomal protein L21 | RL21_ECOLI 1-103
AS CS ES GS | 50S ribosomal protein L22 | RL22_ECOLI 1-110
AT CT ET GT | 50S ribosomal protein L23 | RL23_ECOLI 1-100
AU CU EU GU | 50S ribosomal protein L24 | RL24_ECOLI 0-103
AV CV EV GV | 50S ribosomal protein L25 | RL25_ECOLI 1-94
AW CW EW GW | 50S ribosomal protein L27 | RL27_ECOLI 0-84
AX CX EX GX | 50S ribosomal protein L28 | RL28_ECOLI 0-77
AY CY EY GY | 50S ribosomal protein L29 | RL29_ECOLI 1-63
AZ CZ EZ GZ | 50S ribosomal protein L30 | RL30_ECOLI 0-58
BA DA FA HA | 16S rRNA |
BB DB FB HB | 30S ribosomal protein S2 | RS2_ECOLI 0-240
BC DC FC HC | 30S ribosomal protein S3 | RS3_ECOLI 1-233
BD DD FD HD | 30S ribosomal protein S4 | RS4_ECOLI 1-206
BE DE FE HE | 30S ribosomal protein S5 | RS5_ECOLI 1-167
BF DF FF HF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
BG DG FG HG | 30S ribosomal protein S7 | RS7_ECOLI 1-179
BH DH FH HH | 30S ribosomal protein S8 | RS8_ECOLI 1-130
BI DI FI HI | 30S ribosomal protein S9 | RS9_ECOLI 1-130
BJ DJ FJ HJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
BK DK FK HK | 30S ribosomal protein S11 | RS11_ECOLI 1-129
BL DL FL HL | 30S ribosomal protein S12 | RS12_ECOLI 1-124
BM DM FM HM | 30S ribosomal protein S13 | RS13_ECOLI 1-118
BN DN FN HN | 30S ribosomal protein S14 | RS14_ECOLI 1-101
BO DO FO HO | 30S ribosomal protein S15 | RS15_ECOLI 1-89
BP DP FP HP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
BQ DQ FQ HQ | 30S ribosomal protein S17 | RS17_ECOLI 1-84
BR DR FR HR | 30S ribosomal protein S18 | RS18_ECOLI 1-75
BS DS FS HS | 30S ribosomal protein S19 | RS19_ECOLI 1-92
BT DT FT HT | 30S ribosomal protein S20 | RS20_ECOLI 1-87
BU DU FU HU | 30S ribosomal protein S21 | RS21_ECOLI 1-71
BV DV FV HV | Elongation factor G | EFG_ECOLI 1-704
BW DW FW HW | Viomycin |
Non-standard residues in 4v9o #9
---
GCP — phosphomethylphosphonic acid guanylate ester
MG — magnesium ion
UAL — (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
ZN — zinc ion
4v9o mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> open 4V7D
Summary of feedback from opening 4V7D fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for U /AB:1
Atom OP2 has no neighbors to form bonds with according to residue template for
U /AB:1
4v7d title:
Structure of the Ribosome with Elongation Factor G Trapped in the Pre-
Translocation State (pre-translocation 70S*tRNA*EF-G structure) [more info...]
Chain information for 4v7d #10
---
Chain | Description | UniProt
A1 | 50S ribosomal protein L28 | RL28_ECOLI 1-77
A2 | 50S ribosomal protein L29 | RL29_ECOLI 1-63
A3 | 50S ribosomal protein L30 | RL30_ECOLI 1-58
A4 | 50S ribosomal protein L32 | RL32_ECOLI 1-56
A5 | 50S ribosomal protein L33 | RL33_ECOLI 1-54
A6 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
A7 | 50S ribosomal protein L35 | RL35_ECOLI 1-64
A8 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
AA | 23S ribosomal RNA |
AB | 5S ribosomal RNA |
AC | 50S ribosomal protein L1 | RL1_ECOLI 2-234
AD | 50S ribosomal protein L2 | RL2_ECOLI 1-272
AE | 50S ribosomal protein L3 | RL3_ECOLI 1-209
AF | 50S ribosomal protein L4 | RL4_ECOLI 1-201
AG | 50S ribosomal protein L5 | RL5_ECOLI 1-178
AH | 50S ribosomal protein L6 | RL6_ECOLI 1-176
AI | 50S ribosomal protein L9 | RL9_ECOLI 1-149
AJ | 50S ribosomal protein L10 | RL10_ECOLI 1-165
AK | 50S ribosomal protein L11 | RL11_ECOLI 1-141
AL | 50S ribosomal protein L12 | RL7_ECOLI 2-121
AM | 50S ribosomal protein L13 | RL13_ECOLI 1-142
AN | 50S ribosomal protein L14 | RL14_ECOLI 1-123
AO | 50S ribosomal protein L15 | RL15_ECOLI 1-144
AP | 50S ribosomal protein L16 | RL16_ECOLI 1-136
AQ | 50S ribosomal protein L17 | RL17_ECOLI 1-127
AR | 50S ribosomal protein L18 | RL18_ECOLI 1-117
AS | 50S ribosomal protein L19 | RL19_ECOLI 1-114
AT | 50S ribosomal protein L20 | RL20_ECOLI 1-117
AU | 50S ribosomal protein L21 | RL21_ECOLI 1-103
AV | 50S ribosomal protein L22 | RL22_ECOLI 1-110
AW | 50S ribosomal protein L23 | RL23_ECOLI 1-100
AX | 50S ribosomal protein L24 | RL24_ECOLI 1-103
AY | 50S ribosomal protein L25 | RL25_ECOLI 1-94
AZ | 50S ribosomal protein L27 | RL27_ECOLI -2-81
BA | 16S ribosomal RNA |
BB | 30S ribosomal protein S2 | RS2_ECOLI 1-240
BC | 30S ribosomal protein S3 | RS3_ECOLI 1-232
BD | 30S ribosomal protein S4 | RS4_ECOLI 1-205
BE | 30S ribosomal protein S5 | RS5_ECOLI 1-166
BF | 30S ribosomal protein S6 | RS6_ECOLI 1-131
BG | 30S ribosomal protein S7 | RS7_ECOLI 1-178
BH | 30S ribosomal protein S8 | RS8_ECOLI 1-129
BI | 30S ribosomal protein S9 | RS9_ECOLI 1-129
BJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
BK | 30S ribosomal protein S11 | RS11_ECOLI 1-128
BL | 30S ribosomal protein S12 | RS12_ECOLI 1-123
BM | 30S ribosomal protein S13 | RS13_ECOLI 1-117
BN | 30S ribosomal protein S14 | RS14_ECOLI 1-101
BO | 30S ribosomal protein S15 | RS15_ECOLI 1-88
BP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
BQ | 30S ribosomal protein S17 | RS17_ECOLI 1-83
BR | 30S ribosomal protein S18 | RS18_ECOLI 1-74
BS | 30S ribosomal protein S19 | RS19_ECOLI 1-91
BT | 30S ribosomal protein S20 | RS20_ECOLI 1-86
BU | 30S ribosomal protein S21 | RS21_ECOLI 1-70
BV BW | tRNA |
BX | mRNA |
BY | viomycin |
BZ | Elongation Factor G | EFG_ECOLI 2-704
Non-standard residues in 4v7d #10
---
UAL — (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
ZN — zinc ion
> open 4V7B
Summary of feedback from opening 4V7B fetched from pdb
---
note | Fetching compressed mmCIF 4v7b from http://files.rcsb.org/download/4v7b.cif
4v7b title:
Visualization of two tRNAs trapped in transit during EF-G-mediated
translocation [more info...]
Chain information for 4v7b #11
---
Chain | Description | UniProt
AA | 16S ribosomal RNA |
AB | 30S ribosomal protein S2 | RS2_ECOLI 0-240
AC | 30S ribosomal protein S3 | RS3_ECOLI 1-233
AD | 30S ribosomal protein S4 | RS4_ECOLI 1-206
AE | 30S ribosomal protein S5 | RS5_ECOLI 1-167
AF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
AG | 30S ribosomal protein S7 | RS7_ECOLI 1-179
AH | 30S ribosomal protein S8 | RS8_ECOLI 1-130
AI | 30S ribosomal protein S9 | RS9_ECOLI 1-130
AJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
AK | 30S ribosomal protein S11 | RS11_ECOLI 1-129
AL | 30S ribosomal protein S12 | RS12_ECOLI 1-124
AM | 30S ribosomal protein S13 | RS13_ECOLI 1-118
AN | 30S ribosomal protein S14 | RS14_ECOLI 1-101
AO | 30S ribosomal protein S15 | RS15_ECOLI 1-89
AP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
AQ | 30S ribosomal protein S17 | RS17_ECOLI 1-84
AR | 30S ribosomal protein S18 | RS18_ECOLI 1-75
AS | 30S ribosomal protein S19 | RS19_ECOLI 1-92
AT | 30S ribosomal protein S20 | RS20_ECOLI 1-87
AU | 30S ribosomal protein S21 | RS21_ECOLI 1-71
AV | modified formyl-methionine specific initiator transfer RNA |
AW | formyl-methionine specific initiator transfer RNA |
AX | messenger RNA |
AY | Elongation Factor G | EFG_ECOLI 1-704
B0 | 50S ribosomal protein L32 | RL32_ECOLI 0-56
B1 | 50S ribosomal protein L33 | RL33_ECOLI 0-54
B2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
B3 | 50S ribosomal protein L35 | RL35_ECOLI 0-64
B4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
B5 | 50S ribosomal protein L10 | RL10_ECOLI 1-165
B6 | 50S ribosomal protein L7/L12 | RL7_ECOLI 0-120
BA | 23S ribosomal RNA |
BB | 5S ribosomal RNA |
BC | 50S ribosomal protein L2 | RL2_ECOLI 0-272
BD | 50S ribosomal protein L3 | RL3_ECOLI 1-209
BE | 50S ribosomal protein L4 | RL4_ECOLI 1-201
BF | 50S ribosomal protein L5 | RL5_ECOLI 0-178
BG | 50S ribosomal protein L6 | RL6_ECOLI 0-176
BH | 50S ribosomal protein L9 | RL9_ECOLI 1-50
BI | 50S ribosomal protein L11 | RL11_ECOLI 0-141
BJ | 50S ribosomal protein L13 | RL13_ECOLI 1-142
BK | 50S ribosomal protein L14 | RL14_ECOLI 1-123
BL | 50S ribosomal protein L15 | RL15_ECOLI 1-144
BM | 50S ribosomal protein L16 | RL16_ECOLI 1-136
BN | 50S ribosomal protein L17 | RL17_ECOLI 1-127
BO | 50S ribosomal protein L18 | RL18_ECOLI 1-117
BP | 50S ribosomal protein L19 | RL19_ECOLI 0-114
BQ | 50S ribosomal protein L20 | RL20_ECOLI 0-117
BR | 50S ribosomal protein L21 | RL21_ECOLI 1-103
BS | 50S ribosomal protein L22 | RL22_ECOLI 1-110
BT | 50S ribosomal protein L23 | RL23_ECOLI 1-100
BU | 50S ribosomal protein L24 | RL24_ECOLI 0-103
BV | 50S ribosomal protein L25 | RL25_ECOLI 1-94
BW | 50S ribosomal protein L27 | RL27_ECOLI 0-84
BX | 50S ribosomal protein L28 | RL28_ECOLI 0-77
BY | 50S ribosomal protein L29 | RL29_ECOLI 1-63
BZ | 50S ribosomal protein L30 | RL30_ECOLI 0-58
Non-standard residues in 4v7b #11
---
FUA — fusidic acid
GDP — guanosine-5'-diphosphate
> hide #1 models
> show #!2 models
> hide #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> select add #8
595552 atoms, 641007 bonds, 20010 pseudobonds, 48148 residues, 5 models
selected
> ui mousemode right "translate selected models"
> select add #1
600420 atoms, 645845 bonds, 20010 pseudobonds, 48760 residues, 5 models
selected
> show #1 models
> hide #1 models
> select subtract #1
590573 atoms, 635608 bonds, 20010 pseudobonds, 47798 residues, 4 models
selected
> view matrix models #8,1,0,0,-8.0053,0,1,0,17.307,0,0,1,-7.4662
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.25296,-0.51092,0.82157,32.85,-0.88476,0.22139,0.4101,146.66,-0.39142,-0.83063,-0.39603,276.64
> view matrix models
> #8,-0.38093,0.22877,0.89586,-22.843,-0.42813,0.81514,-0.3902,115.36,-0.81951,-0.53218,-0.21257,251.78
> view matrix models
> #8,-0.40651,0.65735,0.63454,-50.369,0.019722,0.70066,-0.71322,128.83,-0.91343,-0.27742,-0.29779,234.32
> view matrix models
> #8,-0.98494,0.12219,-0.12232,143.42,0.17222,0.75612,-0.63137,101.17,0.015341,-0.64293,-0.76577,258.32
> view matrix models
> #8,-0.57399,-0.80584,-0.14543,236.06,-0.81007,0.53286,0.24462,116.86,-0.11963,0.25822,-0.95865,169.98
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.57399,-0.80584,-0.14543,497.75,-0.81007,0.53286,0.24462,264.36,-0.11963,0.25822,-0.95865,286.73
> view matrix models
> #8,-0.57399,-0.80584,-0.14543,541.63,-0.81007,0.53286,0.24462,241.13,-0.11963,0.25822,-0.95865,266.08
> view matrix models
> #8,-0.57399,-0.80584,-0.14543,549.47,-0.81007,0.53286,0.24462,238.67,-0.11963,0.25822,-0.95865,250.2
> view matrix models
> #8,-0.57399,-0.80584,-0.14543,521.47,-0.81007,0.53286,0.24462,255.28,-0.11963,0.25822,-0.95865,263.74
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.58983,-0.73851,-0.32666,532.53,-0.8055,0.50938,0.30283,252.01,-0.057247,0.44174,-0.89532,228.14
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.58983,-0.73851,-0.32666,538.84,-0.8055,0.50938,0.30283,251.45,-0.057247,0.44174,-0.89532,193.97
> fitmap #8 inMap #2
Fit molecule 4v9p (#8) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 590573 atoms
average map value = 0.1667, steps = 2000
shifted from previous position = 13
rotated from previous position = 20.9 degrees
atoms outside contour = 498656, contour level = 0.31892
Position of 4v9p (#8) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.73943756 -0.55422171 -0.38219153 518.20395936
-0.65764745 0.47322753 0.58613609 214.28962746
-0.14398579 0.68475834 -0.71440471 145.08969087
Axis 0.35502925 -0.85751448 -0.37232130
Axis point 298.37353636 0.00000000 47.88698189
Rotation angle (degrees) 172.01619843
Shift along axis -53.79887841
> select subtract #8
Nothing selected
> select #8
590573 atoms, 635608 bonds, 20010 pseudobonds, 47798 residues, 4 models
selected
> hide sel atoms
> select #8/BV
5353 atoms, 5452 bonds, 4 pseudobonds, 692 residues, 3 models selected
> show sel atoms
> fitmap sel inMap #2
Fit molecule 4v9p (#8) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5353 atoms
average map value = 0.1576, steps = 128
shifted from previous position = 6.61
rotated from previous position = 6.67 degrees
atoms outside contour = 4474, contour level = 0.31892
Position of 4v9p (#8) relative to cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
-0.67283497 -0.56559296 -0.47686233 516.36595751
-0.73214672 0.41665153 0.53885310 243.41316762
-0.10608611 0.71169241 -0.69443475 129.38763931
Axis 0.39131508 -0.83945214 -0.37708435
Axis point 307.58312712 0.00000000 45.73954190
Rotation angle (degrees) 167.24137990
Shift along axis -51.06197149
> select add #8
590573 atoms, 635608 bonds, 20010 pseudobonds, 47798 residues, 4 models
selected
> show sel cartoons
> select #8
590573 atoms, 635608 bonds, 20010 pseudobonds, 47798 residues, 4 models
selected
> hide sel atoms
> hide sel cartoons
> select #8/BV
5353 atoms, 5452 bonds, 4 pseudobonds, 692 residues, 3 models selected
> show sel cartoons
> select add #8
590573 atoms, 635608 bonds, 20010 pseudobonds, 47798 residues, 4 models
selected
> select subtract #8
Nothing selected
> select #8
590573 atoms, 635608 bonds, 20010 pseudobonds, 47798 residues, 4 models
selected
> show sel atoms
> select subtract #8
Nothing selected
> hide #!8 atoms
> hide #!8 models
> show #!9 models
> select add #9
592086 atoms, 637125 bonds, 19926 pseudobonds, 47994 residues, 4 models
selected
> select subtract #9
Nothing selected
> hide #!9 models
> show #!10 models
> select add #10
153817 atoms, 166691 bonds, 3130 pseudobonds, 11463 residues, 4 models
selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,-127.35,0,1,0,5.2707,0,0,1,-16.348
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.21073,0.11553,-0.97069,191.31,0.81035,-0.53473,-0.23956,167.27,-0.54674,-0.83709,0.019062,356.53
> view matrix models
> #10,-0.097879,0.18357,-0.97812,161.51,0.80946,-0.55708,-0.18555,163.82,-0.57896,-0.80991,-0.094066,372.92
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.097879,0.18357,-0.97812,349.14,0.80946,-0.55708,-0.18555,203.21,-0.57896,-0.80991,-0.094066,537.48
> view matrix models
> #10,-0.097879,0.18357,-0.97812,321.7,0.80946,-0.55708,-0.18555,225.75,-0.57896,-0.80991,-0.094066,488.7
> view matrix models
> #10,-0.097879,0.18357,-0.97812,364.58,0.80946,-0.55708,-0.18555,239.7,-0.57896,-0.80991,-0.094066,467.46
> view matrix models
> #10,-0.097879,0.18357,-0.97812,364.59,0.80946,-0.55708,-0.18555,239.01,-0.57896,-0.80991,-0.094066,467.33
> fitmap sel inMap #2
Fit molecule 4v7d (#10) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153817 atoms
average map value = 0.4541, steps = 2000
shifted from previous position = 16.3
rotated from previous position = 10.6 degrees
atoms outside contour = 73218, contour level = 0.31892
Position of 4v7d (#10) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.02483108 0.04930411 -0.99847509 376.95034663
0.80056074 -0.59917345 -0.00967769 205.23723409
-0.59873692 -0.79909966 -0.05434906 463.74020186
Axis -0.68009050 -0.34437620 0.64721089
Axis point 0.00000000 120.33669799 365.14482467
Rotation angle (degrees) 144.52271959
Shift along axis -26.90145895
> fitmap sel inMap #2
Fit molecule 4v7d (#10) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 153817 atoms
average map value = 0.4542, steps = 2000
shifted from previous position = 0.014
rotated from previous position = 0.0192 degrees
atoms outside contour = 73228, contour level = 0.31892
Position of 4v7d (#10) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.02471409 0.04899150 -0.99849338 377.01587146
0.80054787 -0.59919213 -0.00958495 205.21561763
-0.59875896 -0.79910487 -0.05402853 463.69805292
Axis -0.68002296 -0.34429604 0.64732450
Axis point 0.00000000 120.35053364 365.18914735
Rotation angle (degrees) 144.51359572
Shift along axis -26.87126314
> select subtract #10
Nothing selected
> select #10/BZ
5301 atoms, 5398 bonds, 2 pseudobonds, 686 residues, 2 models selected
> fitmap sel inMap #2
Fit molecule 4v7d (#10) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5301 atoms
average map value = 0.138, steps = 224
shifted from previous position = 6.58
rotated from previous position = 14.4 degrees
atoms outside contour = 4684, contour level = 0.31892
Position of 4v7d (#10) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.14698588 -0.13152240 -0.98035554 440.48642312
0.79632523 -0.60364790 -0.03840988 213.08169217
-0.58673781 -0.78632757 0.19346233 429.35559119
Axis -0.59591403 -0.31362051 0.73927576
Axis point 343.33324052 301.03394000 0.00000000
Rotation angle (degrees) 141.13126814
Shift along axis -11.90664539
> show sel cartoons
> select #10
153817 atoms, 166691 bonds, 3130 pseudobonds, 11463 residues, 4 models
selected
> hide sel atoms
> select subtract #10
Nothing selected
> show #!5 models
> hide #!10 models
> show #!10 models
> hide #!5 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #!11 models
> hide #!10 models
> show #!2 models
> hide #1 models
> select add #11
150958 atoms, 163717 bonds, 4589 pseudobonds, 11153 residues, 3 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.34738,-0.70859,0.61419,18.468,-0.13269,0.61125,0.78024,27.866,-0.92829,-0.35254,0.11831,-38.31
> view matrix models
> #11,0.89614,-0.22014,0.38532,13.519,0.086253,0.93813,0.33536,12.884,-0.43531,-0.2673,0.85968,-7.9159
> view matrix models
> #11,0.31203,-0.73156,0.60618,17.95,-0.15529,0.59019,0.79219,28.163,-0.9373,-0.34132,0.070558,-40.124
> view matrix models
> #11,0.96481,-0.11426,0.23682,8.4901,0.0689,0.97904,0.19167,7.4874,-0.25376,-0.16861,0.95246,-3.3542
> view matrix models
> #11,0.77677,0.069751,-0.62591,-24.44,-0.35752,0.86702,-0.34706,-15.03,0.51847,0.49336,0.69841,-7.8158
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.55769,0.81963,-0.1311,-22.751,0.4015,-0.40461,-0.82164,0.018664,-0.72648,0.40558,-0.55473,-66.747
> view matrix models
> #11,0.32195,0.53244,-0.78285,-43.284,0.92049,0.017396,0.39039,41.078,0.22148,-0.84629,-0.4845,-31.626
> view matrix models
> #11,-0.178,0.015071,-0.98391,-50.733,0.82664,0.54472,-0.14121,15.434,0.53383,-0.83848,-0.10942,-14.724
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.178,0.015071,-0.98391,206.18,0.82664,0.54472,-0.14121,262.66,0.53383,-0.83848,-0.10942,228.35
> view matrix models
> #11,-0.178,0.015071,-0.98391,216.65,0.82664,0.54472,-0.14121,261.54,0.53383,-0.83848,-0.10942,244.36
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.31599,-0.079426,-0.94543,216.91,0.63896,0.71881,-0.27394,251.84,0.70134,-0.69066,-0.17638,242.96
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.31599,-0.079426,-0.94543,213.31,0.63896,0.71881,-0.27394,235.98,0.70134,-0.69066,-0.17638,246.31
> view matrix models
> #11,-0.31599,-0.079426,-0.94543,208.98,0.63896,0.71881,-0.27394,237.19,0.70134,-0.69066,-0.17638,245.12
> fitmap sel inMap #2
Fit molecule 4v7b (#11) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 150958 atoms
average map value = 0.5328, steps = 380
shifted from previous position = 21.6
rotated from previous position = 17.9 degrees
atoms outside contour = 59398, contour level = 0.31892
Position of 4v7b (#11) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.02285285 -0.02670360 -0.99938214 227.58490064
0.62372894 0.78085102 -0.03512719 232.09910020
0.78130656 -0.62414634 -0.00118888 237.09789756
Axis -0.29671124 -0.89700031 0.32764749
Axis point -73.56163456 0.00000000 244.21917974
Rotation angle (degrees) 96.98418396
Shift along axis -198.03543281
> select subtract #11
Nothing selected
> select #11/AY
5259 atoms, 5361 bonds, 1 pseudobond, 673 residues, 2 models selected
> fitmap sel inMap #2
Fit molecule 4v7b (#11) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5259 atoms
average map value = 0.1587, steps = 160
shifted from previous position = 7.31
rotated from previous position = 12.9 degrees
atoms outside contour = 4494, contour level = 0.31892
Position of 4v7b (#11) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.04550852 -0.21239733 -0.97612313 237.08915693
0.51704025 0.83106522 -0.20493903 221.93473722
0.85475045 -0.51402143 0.07199740 233.41813023
Axis -0.15493467 -0.91776753 0.36564738
Axis point -47.36184530 0.00000000 269.00375827
Rotation angle (degrees) 94.08423251
Shift along axis -155.06909813
> hide #!11 models
> show #!11 models
> fitmap sel inMap #2
Fit molecule 4v7b (#11) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5259 atoms
average map value = 0.1587, steps = 64
shifted from previous position = 0.0283
rotated from previous position = 0.049 degrees
atoms outside contour = 4491, contour level = 0.31892
Position of 4v7b (#11) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.04605236 -0.21190515 -0.97620459 237.02389777
0.51741740 0.83087287 -0.20476701 221.97268889
0.85449306 -0.51453526 0.07137974 233.38739480
Axis -0.15528603 -0.91772403 0.36560752
Axis point -47.35124602 0.00000000 268.85476495
Rotation angle (degrees) 94.12311723
Shift along axis -155.18798214
> show sel cartoons
> select #11
150958 atoms, 163717 bonds, 4589 pseudobonds, 11153 residues, 3 models
selected
> hide sel atoms
> show #!10 models
> select subtract #11
Nothing selected
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> save
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J393_big_mask/EFG_PDBs_compare.cxs
> includeMaps true
> open 3JA1
Summary of feedback from opening 3JA1 fetched from pdb
---
note | Fetching compressed mmCIF 3ja1 from http://files.rcsb.org/download/3ja1.cif
3ja1 title:
Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor G
[more info...]
Chain information for 3ja1 #12
---
Chain | Description | UniProt
L0 | 50S ribosomal protein L29 | RL29_ECOLI 1-63
L1 | 50S ribosomal protein L30 | RL30_ECOLI 1-58
L2 | 50S ribosomal protein L31 | RL31_ECOLI 1-70
L3 | 50S ribosomal protein L32 | RL32_ECOLI 1-56
L4 | 50S ribosomal protein L33 | RL33_ECOLI 1-54
L5 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
L6 | 50S ribosomal protein L35 | RL35_ECOLI 1-64
L7 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
LA | 23S ribosomal RNA |
LB | 5S ribosomal RNA |
LC | 50S ribosomal protein L1 | RL1_ECOLI 1-234
LD | 50S ribosomal protein L2 | RL2_ECOLI 1-272
LE | 50S ribosomal protein L3 | RL3_ECOLI 1-209
LF | 50S ribosomal protein L4 | RL4_ECOLI 1-201
LG | 50S ribosomal protein L5 | RL5_ECOLI 1-178
LH | 50S ribosomal protein L6 | RL6_ECOLI 1-176
LI | 50S ribosomal protein L9 | RL9_ECOLI 1-149
LJ | 50S ribosomal protein L10 | RL10_ECOLI 1-164
LK | 50S ribosomal protein L11 | RL11_ECOLI 1-141
LL | 50S ribosomal protein L13 | RL13_ECOLI 1-142
LM | 50S ribosomal protein L14 | RL14_ECOLI 1-123
LN | 50S ribosomal protein L15 | RL15_ECOLI 1-144
LO | 50S ribosomal protein L16 | RL16_ECOLI 1-136
LP | 50S ribosomal protein L17 | RL17_ECOLI 1-127
LQ | 50S ribosomal protein L18 | RL18_ECOLI 1-117
LR | 50S ribosomal protein L19 | RL19_ECOLI 1-114
LS | 50S ribosomal protein L20 | RL20_ECOLI 1-117
LT | 50S ribosomal protein L21 | RL21_ECOLI 1-103
LU | 50S ribosomal protein L22 | RL22_ECOLI 1-110
LV | 50S ribosomal protein L23 | RL23_ECOLI 1-100
LW | 50S ribosomal protein L24 | RL24_ECOLI 1-103
LX | 50S ribosomal protein L25 | RL25_ECOLI 1-94
LY | 50S ribosomal protein L27 | RL27_ECOLI 1-84
LZ | 50S ribosomal protein L28 | RL28_ECOLI 1-77
S1 | mRNA |
S2 | P/E-tRNA |
S3 | Elongation factor G | EFG_ECOLI 1-702
SA | 16S ribosomal RNA |
SB | 30S ribosomal protein S2 | RS2_ECOLI 1-240
SC | 30S ribosomal protein S3 | RS3_ECOLI 1-232
SD | 30S ribosomal protein S4 | RS4_ECOLI 1-205
SE | 30S ribosomal protein S5 | RS5_ECOLI 1-166
SF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
SG | 30S ribosomal protein S7 | RS7_ECOLI 1-178
SH | 30S ribosomal protein S8 | RS8_ECOLI 1-129
SI | 30S ribosomal protein S9 | RS9_ECOLI 1-129
SJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
SK | 30S ribosomal protein S11 | RS11_ECOLI 1-128
SL | 30S ribosomal protein S12 | RS12_ECOLI 1-123
SM | 30S ribosomal protein S13 | RS13_ECOLI 1-117
SN | 30S ribosomal protein S14 | RS14_ECOLI 1-100
SO | 30S ribosomal protein S15 | RS15_ECO57 1-88
SP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
SQ | 30S ribosomal protein S17 | RS17_ECOLI 1-83
SR | 30S ribosomal protein S18 | RS18_ECOLI 1-74
SS | 30S ribosomal protein S19 | RS19_ECOLI 1-91
ST | 30S ribosomal protein S20 | RS20_ECOLI 1-86
SU | 30S ribosomal protein S21 | RS21_ECOLI 1-70
Non-standard residues in 3ja1 #12
---
GTP — guanosine-5'-triphosphate
> open 3J9Z
3j9z title:
Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor G
[more info...]
Chain information for 3j9z #13
---
Chain | Description | UniProt
L1 | 50S ribosomal protein L32 | RL32_ECOLI 1-56
L2 | 50S ribosomal protein L33 | RL33_ECOLI 1-54
L3 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
L4 | 50S ribosomal protein L35 | RL35_ECOLI 1-64
L5 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
L6 | 50S ribosomal protein L4 | RL4_ECOLI 1-201
L7 | 50S ribosomal protein L5 | RL5_ECOLI 1-178
L8 | 50S ribosomal protein L6 | RL6_ECOLI 1-176
L9 | 50S ribosomal protein L9 | RL9_ECOLI 1-149
LA | 23S ribosomal RNA |
LB | 5S ribosomal RNA |
LC | 50S ribosomal protein L1 | RL1_ECOLI 1-234
LD | 50S ribosomal protein L10 | RL10_ECOLI 1-164
LE | 50S ribosomal protein L11 | RL11_ECOLI 1-141
LF | 50S ribosomal protein L13 | RL13_ECOLI 1-142
LG | 50S ribosomal protein L14 | RL14_ECOLI 1-123
LH | 50S ribosomal protein L15 | RL15_ECOLI 1-144
LI | 50S ribosomal protein L16 | RL16_ECOLI 1-136
LJ | 50S ribosomal protein L17 | RL17_ECOLI 1-127
LK | 50S ribosomal protein L18 | RL18_ECOLI 1-117
LM | 50S ribosomal protein L19 | RL19_ECOLI 1-114
LN | 50S ribosomal protein L2 | RL2_ECOLI 1-272
LO | 50S ribosomal protein L20 | RL20_ECOLI 1-117
LP | 50S ribosomal protein L21 | RL21_ECOLI 1-103
LQ | 50S ribosomal protein L22 | RL22_ECOLI 1-110
LR | 50S ribosomal protein L23 | RL23_ECOLI 1-100
LS | 50S ribosomal protein L24 | RL24_ECOLI 1-103
LT | 50S ribosomal protein L25 | RL25_ECOLI 1-94
LU | 50S ribosomal protein L27 | RL27_ECOLI 1-84
LV | 50S ribosomal protein L28 | RL28_ECOLI 1-77
LW | 50S ribosomal protein L29 | RL29_ECOLI 1-63
LX | 50S ribosomal protein L3 | RL3_ECOLI 1-209
LY | 50S ribosomal protein L30 | RL30_ECOLI 1-58
LZ | 50S ribosomal protein L31 | RL31_ECOLI 1-70
S1 | Elongation factor G | EFG_ECOLI 1-702
S6 | P-tRNA |
S7 | E-tRNA |
SA | 16S ribosomal RNA |
SB | 30S ribosomal protein S2 | RS2_ECOLI 1-240
SC | 30S ribosomal protein S3 | RS3_ECOLI 1-232
SD | 30S ribosomal protein S4 | RS4_ECOLI 1-205
SE | 30S ribosomal protein S5 | RS5_ECOLI 1-166
SF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
SG | 30S ribosomal protein S7 | RS7_ECOLI 1-178
SH | 30S ribosomal protein S8 | RS8_ECOLI 1-129
SI | 30S ribosomal protein S9 | RS9_ECOLI 1-129
SJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
SK | 30S ribosomal protein S11 | RS11_ECOLI 1-128
SL | 30S ribosomal protein S12 | RS12_ECOLI 1-123
SM | 30S ribosomal protein S13 | RS13_ECOLI 1-117
SN | 30S ribosomal protein S14 | RS14_ECOLI 1-100
SO | 30S ribosomal protein S15 | RS15_ECO57 1-88
SP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
SQ | 30S ribosomal protein S17 | RS17_ECOLI 1-83
SR | 30S ribosomal protein S18 | RS18_ECOLI 1-74
SS | 30S ribosomal protein S19 | RS19_ECOLI 1-91
ST | 30S ribosomal protein S20 | RS20_ECOLI 1-86
SU | 30S ribosomal protein S21 | RS21_ECOLI 1-70
Non-standard residues in 3j9z #13
---
GTP — guanosine-5'-triphosphate
> open 3J0E
Summary of feedback from opening 3J0E fetched from pdb
---
note | Fetching compressed mmCIF 3j0e from http://files.rcsb.org/download/3j0e.cif
3j0e title:
Models for the T. thermophilus ribosome recycling factor and the E. coli
elongation factor G bound to the E. coli post-termination complex [more
info...]
Chain information for 3j0e #14
---
Chain | Description | UniProt
A | ribosomal 23S RNA |
B | ribosomal 23S RNA |
C | ribosomal 23S RNA |
D | ribosomal 23S RNA |
E | ribosomal 16S RNA |
F | 30S ribosomal protein S12 | RS12_ECOLI 1-123
G | Ribosome-recycling factor | RRF_THET8 1-185
H | Elongation factor G | EFG_ECOLI 2-703
e | ribosomal 16S RNA |
> open 2RDO
2rdo title:
50S subunit with EF-G(GDPNP) and RRF bound [more info...]
Chain information for 2rdo #15
---
Chain | Description | UniProt
0 | 50S ribosomal protein L32 | RL32_ECOLI 1-56
1 | 50S ribosomal protein L33 | RL33_ECOLI 1-54
2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
3 | 50S ribosomal protein L35 | RL35_ECOLI 1-64
4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
7 | Elongation factor G | EFG_ECOLI 1-704
8 | Ribosome recycling factor | RRF_ECOLI 1-185
9 | 50S ribosomal protein L1 | RL1_ECOLI 1-233
A | 5S RIBOSOMAL RNA |
B | 23S RIBOSOMAL RNA |
C | 50S ribosomal protein L2 | RL2_ECOLI 1-272
D | 50S ribosomal protein L3 | RL3_ECOLI 1-209
E | 50S ribosomal protein L4 | RL4_ECOLI 1-201
F | 50S ribosomal protein L5 | RL5_ECOLI 1-178
G | 50S ribosomal protein L6 | RL6_ECOLI 1-176
H | 50S ribosomal protein L9 | RL9_ECOLI 1-149
I | 50S ribosomal protein L11 | RL11_ECOLI 1-141
J | 50S ribosomal protein L13 | RL13_ECOLI 1-142
K | 50S ribosomal protein L14 | RL14_ECOLI 1-123
L | 50S ribosomal protein L15 | RL15_ECOLI 1-144
M | 50S ribosomal protein L16 | RL16_ECOLI 1-136
N | 50S ribosomal protein L17 | RL17_ECOLI 1-127
O | 50S ribosomal protein L18 | RL18_ECOLI 1-117
P | 50S ribosomal protein L19 | RL19_ECOLI 1-114
Q | 50S ribosomal protein L20 | RL20_ECOLI 1-117
R | 50S ribosomal protein L21 | RL21_ECOLI 1-103
S | 50S ribosomal protein L22 | RL22_ECOLI 1-110
T | 50S ribosomal protein L23 | RL23_ECOLI 1-100
U | 50S ribosomal protein L24 | RL24_ECOLI 1-103
V | 50S ribosomal protein L25 | RL25_ECOLI 1-94
W | 50S ribosomal protein L27 | RL27_ECOLI 1-84
X | 50S ribosomal protein L29 | RL29_ECOLI 1-63
Y | 50S ribosomal protein L30 | RL30_ECOLI 1-58
Z | 50S ribosomal protein L31 | RL31_ECOLI 1-70
> hide #!10 models
> hide #!15 models
> hide #!14 models
> select add #13
156714 atoms, 169620 bonds, 4642 pseudobonds, 11843 residues, 2 models
selected
> select add #12
312841 atoms, 338582 bonds, 9054 pseudobonds, 23659 residues, 4 models
selected
> show #!2 models
> hide #1 models
> ui mousemode right "translate selected models"
> view matrix models
> #12,1,0,0,200.57,0,1,0,-72.467,0,0,1,-63.486,#13,1,0,0,200.57,0,1,0,-72.467,0,0,1,-63.486
> view matrix models
> #12,1,0,0,245.14,0,1,0,-15.525,0,0,1,-11.533,#13,1,0,0,245.14,0,1,0,-15.525,0,0,1,-11.533
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.34505,-0.54521,-0.764,598.65,0.30031,0.83533,-0.46048,44.424,0.88924,-0.070549,0.45196,-57.652,#13,0.34505,-0.54521,-0.764,598.65,0.30031,0.83533,-0.46048,44.424,0.88924,-0.070549,0.45196,-57.652
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.34505,-0.54521,-0.764,444.96,0.30031,0.83533,-0.46048,131.08,0.88924,-0.070549,0.45196,-50.858,#13,0.34505,-0.54521,-0.764,444.96,0.30031,0.83533,-0.46048,131.08,0.88924,-0.070549,0.45196,-50.858
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.10523,-0.30251,-0.94732,467.33,0.57172,0.79784,-0.19127,46.618,0.81367,-0.52148,0.25691,87.308,#13,0.10523,-0.30251,-0.94732,467.33,0.57172,0.79784,-0.19127,46.618,0.81367,-0.52148,0.25691,87.308
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.10523,-0.30251,-0.94732,470.11,0.57172,0.79784,-0.19127,4.2261,0.81367,-0.52148,0.25691,113.62,#13,0.10523,-0.30251,-0.94732,470.11,0.57172,0.79784,-0.19127,4.2261,0.81367,-0.52148,0.25691,113.62
> view matrix models
> #12,0.10523,-0.30251,-0.94732,468.57,0.57172,0.79784,-0.19127,18.555,0.81367,-0.52148,0.25691,120.52,#13,0.10523,-0.30251,-0.94732,468.57,0.57172,0.79784,-0.19127,18.555,0.81367,-0.52148,0.25691,120.52
> view matrix models
> #12,0.10523,-0.30251,-0.94732,481.36,0.57172,0.79784,-0.19127,14.866,0.81367,-0.52148,0.25691,130.14,#13,0.10523,-0.30251,-0.94732,481.36,0.57172,0.79784,-0.19127,14.866,0.81367,-0.52148,0.25691,130.14
> fitmap #14 inMap #2
Fit molecule 3j0e (#14) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 10187 atoms
average map value = 0.1133, steps = 268
shifted from previous position = 36.3
rotated from previous position = 9.74 degrees
atoms outside contour = 8861, contour level = 0.31892
Position of 3j0e (#14) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99674146 -0.03726129 0.07154059 21.95292716
0.02618017 0.98833765 0.15001095 -4.97625644
-0.07629586 -0.14764919 0.98609262 65.78055281
Axis -0.87973545 0.43693107 0.18750142
Axis point 0.00000000 453.21063154 41.74683333
Rotation angle (degrees) 9.73990999
Shift along axis -9.15310217
> fitmap #12 inMap #2
Fit molecule 3ja1 (#12) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 156127 atoms
average map value = 0.2709, steps = 544
shifted from previous position = 27.1
rotated from previous position = 18.1 degrees
atoms outside contour = 102878, contour level = 0.31892
Position of 3ja1 (#12) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.12615540 -0.10392769 -0.98655149 467.62297888
0.51610704 0.84242996 -0.15474254 5.12666347
0.84718257 -0.52868779 -0.05263928 182.24720474
Axis -0.18967437 -0.93011570 0.31449710
Axis point 145.46087899 0.00000000 301.00306598
Rotation angle (degrees) 99.68215436
Shift along axis -36.14826551
> fitmap #13 inMap #2
Fit molecule 3j9z (#13) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 156714 atoms
average map value = 0.6462, steps = 356
shifted from previous position = 32.2
rotated from previous position = 21.9 degrees
atoms outside contour = 37812, contour level = 0.31892
Position of 3j9z (#13) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.10517447 0.00931248 -0.99441017 437.63231926
0.59027129 0.80533659 -0.05488860 -18.51176069
0.80032376 -0.59274466 -0.09019774 215.62935688
Axis -0.27419261 -0.91493398 0.29616588
Axis point 119.66819443 0.00000000 296.28689845
Rotation angle (degrees) 101.24576391
Shift along axis -39.19645143
> select subtract #13
156127 atoms, 168962 bonds, 4412 pseudobonds, 11816 residues, 2 models
selected
> select subtract #12
Nothing selected
> hide #!13 models
> select #13/S3
Nothing selected
> select #12/S3
5463 atoms, 5566 bonds, 703 residues, 1 model selected
> fitmap sel inMap #2
Fit molecule 3ja1 (#12) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5463 atoms
average map value = 0.1473, steps = 84
shifted from previous position = 5.52
rotated from previous position = 2.76 degrees
atoms outside contour = 4768, contour level = 0.31892
Position of 3ja1 (#12) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.10956891 -0.14566086 -0.98324847 473.48223670
0.52757454 0.82984386 -0.18172573 4.64421243
0.84241304 -0.53864836 -0.01407813 178.63806017
Axis -0.18041866 -0.92284258 0.34030969
Axis point 148.21416654 0.00000000 308.98694265
Rotation angle (degrees) 98.44741178
Shift along axis -28.91864514
> hide sel atoms
> show sel cartoons
> select #12
156127 atoms, 168962 bonds, 4412 pseudobonds, 11816 residues, 2 models
selected
> hide sel atoms
> select subtract #12
Nothing selected
> show #!13 models
> hide #!12 models
> select add #13
156714 atoms, 169620 bonds, 4642 pseudobonds, 11843 residues, 2 models
selected
> select subtract #13
Nothing selected
> select #13/S1
5463 atoms, 5566 bonds, 703 residues, 1 model selected
> fitmap sel inMap #2
Fit molecule 3j9z (#13) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 5463 atoms
average map value = 0.1479, steps = 336
shifted from previous position = 8.5
rotated from previous position = 8.18 degrees
atoms outside contour = 4721, contour level = 0.31892
Position of 3j9z (#13) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.20014395 -0.08869450 -0.97574365 473.63400110
0.53934125 0.82144719 -0.18529840 7.33585871
0.81795684 -0.56334516 -0.11657108 202.10015046
Axis -0.19510003 -0.92568184 0.32411280
Axis point 146.69262363 -0.00000000 298.24241595
Rotation angle (degrees) 104.33754388
Shift along axis -33.69343413
> undo
[Repeated 1 time(s)]
> fitmap sel inMap #2
Fit molecule 3j9z (#13) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 156714 atoms
average map value = 0.6461, steps = 172
shifted from previous position = 11.4
rotated from previous position = 8.18 degrees
atoms outside contour = 37786, contour level = 0.31892
Position of 3j9z (#13) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.10526569 0.00933969 -0.99440027 437.65326672
0.59015887 0.80541761 -0.05490860 -18.48786151
0.80039467 -0.59263414 -0.09029474 215.60702735
Axis -0.27412905 -0.91497502 0.29609792
Axis point 119.69308479 0.00000000 296.26918159
Rotation angle (degrees) 101.24889537
Shift along axis -39.21675172
> select subtract #13
Nothing selected
> select #13/S1
5463 atoms, 5566 bonds, 703 residues, 1 model selected
> show sel cartoons
> select #13
156714 atoms, 169620 bonds, 4642 pseudobonds, 11843 residues, 2 models
selected
> hide sel atoms
> select subtract #13
Nothing selected
> show #!9 models
> hide #!9 models
> hide #!13 models
> show #!13 models
> show #!13 atoms
> hide #!13 atoms
> show #!14 models
> hide #!13 models
> select add #14
10187 atoms, 10592 bonds, 97 pseudobonds, 1118 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.99674,-0.037261,0.071541,-93.301,0.02618,0.98834,0.15001,45.387,-0.076296,-0.14765,0.98609,12.416
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.50468,-0.0042133,-0.8633,109.38,-0.13117,0.988,-0.081506,102.82,0.85328,0.15438,0.49807,-123.6
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.50468,-0.0042133,-0.8633,315.52,-0.13117,0.988,-0.081506,59.736,0.85328,0.15438,0.49807,-28.495
> view matrix models
> #14,0.50468,-0.0042133,-0.8633,315.24,-0.13117,0.988,-0.081506,59.81,0.85328,0.15438,0.49807,-28.994
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.31102,-0.050233,-0.94907,366.79,0.044509,0.99828,-0.038251,24.255,0.94936,-0.030346,0.31272,19.372
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.31102,-0.050233,-0.94907,366.76,0.044509,0.99828,-0.038251,30.13,0.94936,-0.030346,0.31272,18.922
> fitmap sel inMap #2
Fit molecule 3j0e (#14) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 10187 atoms
average map value = 0.1275, steps = 348
shifted from previous position = 6.39
rotated from previous position = 16.2 degrees
atoms outside contour = 8789, contour level = 0.31892
Position of 3j0e (#14) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.30429741 -0.00589068 -0.95255886 354.77719111
0.29262734 0.95220632 0.08759207 -15.29791408
0.90651659 -0.30539880 0.29147769 82.00000481
Axis -0.20431406 -0.96652435 0.15519807
Axis point 118.02922018 0.00000000 276.59724109
Rotation angle (degrees) 74.09812399
Shift along axis -44.97391809
> select subtract #14
Nothing selected
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!15 models
> hide #!14 models
> select add #15
7428 atoms, 7394 pseudobonds, 7428 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,377.8,0,1,0,52.083,0,0,1,234.13
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.55315,0.57307,-0.60466,391.6,0.1183,0.66442,0.73793,49.949,0.82464,-0.47972,0.29974,203.88
> view matrix models
> #15,0.52329,0.36919,-0.76803,387.37,0.3815,0.70441,0.59855,44.289,0.76199,-0.60622,0.22777,202.37
> view matrix models
> #15,0.25997,0.11007,-0.95932,386.6,0.7753,0.56843,0.27532,31.532,0.57562,-0.81533,0.062441,201.14
> view matrix models
> #15,0.30415,0.2335,-0.92357,388.13,0.80785,0.45056,0.37995,29.71,0.50484,-0.86167,-0.051594,200.83
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.30415,0.2335,-0.92357,361.44,0.80785,0.45056,0.37995,184.56,0.50484,-0.86167,-0.051594,153.07
> view matrix models
> #15,0.30415,0.2335,-0.92357,234.84,0.80785,0.45056,0.37995,225.56,0.50484,-0.86167,-0.051594,221.34
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.14148,0.047623,-0.9888,239.96,0.57577,0.81648,-0.043056,233.02,0.80528,-0.57541,-0.14293,219.55
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.14148,0.047623,-0.9888,225.48,0.57577,0.81648,-0.043056,232.36,0.80528,-0.57541,-0.14293,235.5
> fitmap #15 inMap #2
Fit molecule 2rdo (#15) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 7428 atoms
average map value = 0.1469, steps = 140
shifted from previous position = 2.19
rotated from previous position = 2.11 degrees
atoms outside contour = 6076, contour level = 0.31892
Position of 2rdo (#15) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.16254315 0.04577252 -0.98563919 227.55921044
0.54930631 0.83401052 -0.05185590 233.03119470
0.81965987 -0.54984664 -0.16070582 233.87693322
Axis -0.25679706 -0.93093197 0.25965543
Axis point -39.54129831 -0.00000000 221.58959777
Rotation angle (degrees) 104.15933232
Shift along axis -214.64531043
> select #15/7
684 atoms, 683 pseudobonds, 684 residues, 2 models selected
> fitmap sel inMap #2
Fit molecule 2rdo (#15) to map cryosparc_P249_J393_003_volume_map_sharp.mrc
(#2) using 684 atoms
average map value = 0.1242, steps = 88
shifted from previous position = 2.93
rotated from previous position = 4.39 degrees
atoms outside contour = 610, contour level = 0.31892
Position of 2rdo (#15) relative to
cryosparc_P249_J393_003_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.20203520 0.09549096 -0.97471189 225.43815894
0.51872114 0.85461232 -0.02379388 233.72929402
0.83072869 -0.51041086 -0.22219494 226.11325610
Axis -0.25382065 -0.94172237 0.22075793
Axis point -28.23673913 0.00000000 206.88952904
Rotation angle (degrees) 106.54742646
Shift along axis -227.41266826
> select add #15
7428 atoms, 7394 pseudobonds, 7428 residues, 2 models selected
> select subtract #15
Nothing selected
> select #15/7
684 atoms, 683 pseudobonds, 684 residues, 2 models selected
> show sel cartoons
Computing secondary structure
> select #15
7428 atoms, 7394 pseudobonds, 7428 residues, 2 models selected
> hide sel atoms
> select subtract #15
Nothing selected
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!15 models
> show #!10 models
> color #10 #d4d4d4ff
> color #10 #b2b2b2ff
> save
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J393_big_mask/EFG_PDBs_compare.cxs
> includeMaps true
> open 4v7c
Summary of feedback from opening 4v7c fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for U /BB:1
Atom OP2 has no neighbors to form bonds with according to residue template for
U /BB:1
Atom O has no neighbors to form bonds with according to residue template for
VAL /BP:60
note | Fetching compressed mmCIF 4v7c from http://files.rcsb.org/download/4v7c.cif
4v7c title:
Structure of the Ribosome with Elongation Factor G Trapped in the Pre-
Translocation State (pre-translocation 70S*tRNA structure) [more info...]
Chain information for 4v7c #16
---
Chain | Description | UniProt
AA | 16S ribosomal RNA |
AB | 30S ribosomal protein S2 | RS2_ECOLI 1-240
AC | 30S ribosomal protein S3 | RS3_ECOLI 1-232
AD | 30S ribosomal protein S4 | RS4_ECOLI 1-205
AE | 30S ribosomal protein S5 | RS5_ECOLI 1-166
AF | 30S ribosomal protein S6 | RS6_ECOLI 1-131
AG | 30S ribosomal protein S7 | RS7_ECOLI 1-178
AH | 30S ribosomal protein S8 | RS8_ECOLI 1-129
AI | 30S ribosomal protein S9 | RS9_ECOLI 1-129
AJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
AK | 30S ribosomal protein S11 | RS11_ECOLI 1-128
AL | 30S ribosomal protein S12 | RS12_ECOLI 1-123
AM | 30S ribosomal protein S13 | RS13_ECOLI 1-117
AN | 30S ribosomal protein S14 | RS14_ECOLI 1-101
AO | 30S ribosomal protein S15 | RS15_ECOLI 1-88
AP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
AQ | 30S ribosomal protein S17 | RS17_ECOLI 1-83
AR | 30S ribosomal protein S18 | RS18_ECOLI 1-74
AS | 30S ribosomal protein S19 | RS19_ECOLI 1-91
AT | 30S ribosomal protein S20 | RS20_ECOLI 1-86
AU | 30S ribosomal protein S21 | RS21_ECOLI 1-70
AV AW | tRNA |
AX | mRNA |
AY | viomycin |
B1 | 50S ribosomal protein L29 | RL29_ECOLI 1-63
B2 | 50S ribosomal protein L30 | RL30_ECOLI 1-58
B3 | 50S ribosomal protein L32 | RL32_ECOLI 1-56
B4 | 50S ribosomal protein L33 | RL33_ECOLI 1-54
B5 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
B6 | 50S ribosomal protein L35 | RL35_ECOLI 1-64
B7 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
BA | 23S ribosomal RNA |
BB | 5S ribosomal RNA |
BC | 50S ribosomal protein L1 | RL1_ECOLI 2-234
BD | 50S ribosomal protein L2 | RL2_ECOLI 1-272
BE | 50S ribosomal protein L3 | RL3_ECOLI 1-209
BF | 50S ribosomal protein L4 | RL4_ECOLI 1-201
BG | 50S ribosomal protein L5 | RL5_ECOLI 1-178
BH | 50S ribosomal protein L6 | RL6_ECOLI 1-176
BI | 50S ribosomal protein L9 | RL9_ECOLI 1-149
BJ | 50S ribosomal protein L10 | RL10_ECOLI 1-165
BK | 50S ribosomal protein L11 | RL11_ECOLI 1-141
BL | 50S ribosomal protein L13 | RL13_ECOLI 1-142
BM | 50S ribosomal protein L14 | RL14_ECOLI 1-123
BN | 50S ribosomal protein L15 | RL15_ECOLI 1-144
BO | 50S ribosomal protein L16 | RL16_ECOLI 1-136
BP | 50S ribosomal protein L17 | RL17_ECOLI 1-127
BQ | 50S ribosomal protein L18 | RL18_ECOLI 1-117
BR | 50S ribosomal protein L19 | RL19_ECOLI 1-114
BS | 50S ribosomal protein L20 | RL20_ECOLI 1-117
BT | 50S ribosomal protein L21 | RL21_ECOLI 1-103
BU | 50S ribosomal protein L22 | RL22_ECOLI 1-110
BV | 50S ribosomal protein L23 | RL23_ECOLI 1-100
BW | 50S ribosomal protein L24 | RL24_ECOLI 1-103
BX | 50S ribosomal protein L25 | RL25_ECOLI 1-94
BY | 50S ribosomal protein L27 | RL27_ECOLI -2-81
BZ | 50S ribosomal protein L28 | RL28_ECOLI 1-77
Non-standard residues in 4v7c #16
---
UAL — (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
ZN — zinc ion
> hide #!10 models
> close #16
> select #1/AL, W, Bv, Bs, BO
532 atoms, 586 bonds, 28 residues, 1 model selected
> show sel atoms
> hide sel atoms
> open
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/run_001/run_001.cif
Summary of feedback from opening
/media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/run_001/run_001.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for run_001.cif #16
---
Chain | Description
3 | No description available
4 | No description available
7 | No description available
A AW | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AB | No description available
AD | No description available
AE Q | No description available
AG | No description available
AO | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
An | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B3 | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
BN | No description available
BO | No description available
BP BW | No description available
BQ | No description available
BR | No description available
BS BX | No description available
BT | No description available
BU | No description available
BV | No description available
BY | No description available
BZ Bb | No description available
Ba | No description available
Bo | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | No description available
Bw | No description available
Bx | No description available
By | No description available
Bz | No description available
C | 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
T | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
d | No description available
e | No description available
f | No description available
g | No description available
j | No description available
l | No description available
r | No description available
s | No description available
t | No description available
v | No description available
y | No description available
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> style sel stick
Changed 532 atom styles
> hide sel atoms
> select add #16
10684 atoms, 11112 bonds, 1041 residues, 2 models selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> hide #1 models
> select add #1
19999 atoms, 20763 bonds, 1975 residues, 2 models selected
> select subtract #1
10152 atoms, 10526 bonds, 1013 residues, 1 model selected
> select subtract #16
Nothing selected
> show #1 models
> hide #16 models
> select #1/AL, W, Bv, Bs, BO
532 atoms, 586 bonds, 28 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #16 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show sel atoms
> hide sel atoms
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #16 models
> select #16
10152 atoms, 10526 bonds, 1013 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 10152 atom styles
> hide #1 models
> hide #16 models
> show #16 models
> color sel byhetero
> show #1 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide sel atoms
> hide #!2 models
[Repeated 2 time(s)]
> select #16/Ai
446 atoms, 454 bonds, 58 residues, 1 model selected
> select #16/I,H,Ah
548 atoms, 554 bonds, 70 residues, 1 model selected
> voluem zone #2 nearAtoms #16/I,H,Ah newMap true
Unknown command: voluem zone #2 nearAtoms #16/I,H,Ah newMap true
> volume zone #2 nearAtoms #16/I,H,Ah newMap true
Opened cryosparc_P249_J393_003_volume_map_sharp.mrc zone as #17, grid size
440,440,440, pixel 1.06, shown at step 1, values float32
> show #!2 models
> color #2 #b2b2b26e models
> hide #!2 models
> open
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/run_001/run_001_entropy_score.cif
Summary of feedback from opening
/media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/run_001/run_001_entropy_score.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for run_001_entropy_score.cif #18
---
Chain | Description
3 | No description available
4 | No description available
7 | No description available
A AW | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AB | No description available
AD | No description available
AE Q | No description available
AG | No description available
AO | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Am | No description available
An | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B3 | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
BN | No description available
BO | No description available
BP BW | No description available
BQ | No description available
BR | No description available
BS BX | No description available
BT | No description available
BU | No description available
BV | No description available
BY | No description available
BZ Bb | No description available
Ba | No description available
Bo | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | No description available
Bw | No description available
Bx | No description available
By | No description available
Bz | No description available
C | 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
T | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
d | No description available
e | No description available
f | No description available
g | No description available
j | No description available
l | No description available
r | No description available
s | No description available
t | No description available
v | No description available
y | No description available
> hide sel atoms
> select add #18
10700 atoms, 11080 bonds, 1083 residues, 2 models selected
> select add #16
20304 atoms, 21052 bonds, 2026 residues, 2 models selected
> select subtract #16
10152 atoms, 10526 bonds, 1013 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> color bfactor sel
10152 atoms, 1013 residues, atom bfactor range 2.75e-13 to 88.2
> hide #16 models
> hide #!17 models
> hide #1 models
> show #16 models
> hide #18 models
> select subtract #18
Nothing selected
> color bfactor #16
10152 atoms, 1013 residues, atom bfactor range 0 to 100
> color #16 bychain
> show #18 models
> hide #16 models
> show #!10 models
> show #!2 models
> hide #!10 models
> show #!17 models
> view
> show #1 models
> hide #18 models
> hide #!17 models
> show #!17 models
> surface dust #2 size 10.6
> surface dust #17 size 10.6
> hide #!17 models
> show #18 models
> color #2 #b2b2b2ff models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!2 models
> color #18 bychain
> show #1 models
> hide #18 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!10 models
> hide #!10 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #16 models
> show #1,16 atoms
> style #1,16 stick
Changed 19999 atom styles
> hide #1 models
> color #16 byhetero
> select add #16
10152 atoms, 10526 bonds, 1013 residues, 1 model selected
> style sel stick
Changed 10152 atom styles
> color sel byhetero
> select subtract #16
Nothing selected
> show #1 models
> hide #16 models
> hide #1 cartoons
> hide #1 atoms
> show #1 cartoons
> show #18 models
> hide #18 models
> select #1/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, Bv,
> Bs, BO
4441 atoms, 4856 bonds, 280 residues, 1 model selected
> hide sel cartoons
> show #18 models
> hide #18 models
> show #16 models
> hide sel atoms
> select add #16
14593 atoms, 15382 bonds, 1293 residues, 2 models selected
> hide sel atoms
> select #16/Br,Bl, BQ, BJ, Bo, Bn, Bu, Bb, Bp, Bj, BV, A6, Bi, Al, Ao, E, Bm,
> Bq, Bt, Bn, Bk, BM, BN, BR, BK, BS, BI, F,D,A,BL, BP, g, C, B, AL, W, Bv,
> Bs, BO
2642 atoms, 2838 bonds, 197 residues, 1 model selected
> hide #1 models
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide #16 models
> show #16 models
> select #16/
Expected an objects specifier or a keyword
> select #16/BU,B1,Bu,Bv,Bt
731 atoms, 816 bonds, 34 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,Bv,j
751 atoms, 835 bonds, 36 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ
899 atoms, 998 bonds, 43 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2
1048 atoms, 1163 bonds, 50 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,Bx
1200 atoms, 1332 bonds, 57 residues, 1 model selected
> hide sel atoms
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS
1175 atoms, 1303 bonds, 56 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,
Expected an objects specifier or a keyword
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ
1829 atoms, 2037 bonds, 86 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO
1956 atoms, 2177 bonds, 92 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br
2346 atoms, 2613 bonds, 110 residues, 1 model selected
> hide sel cartoons
> select #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR
2468 atoms, 2746 bonds, 116 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN
2685 atoms, 2987 bonds, 126 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP
2943 atoms, 3274 bonds, 138 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY
3112 atoms, 3461 bonds, 146 residues, 1 model selected
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo
3222 atoms, 3584 bonds, 151 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s
3272 atoms, 3632 bonds, 157 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A
3347 atoms, 3707 bonds, 166 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A,Bx,By
3613 atoms, 4005 bonds, 178 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A,Bx,By,J,B
3672 atoms, 4064 bonds, 185 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A,Bx,By,J,B,C
3686 atoms, 4077 bonds, 187 residues, 1 model selected
> hide sel cartoons
> show #!10 models
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A,Bx,By,J,B,C,A9
3823 atoms, 4214 bonds, 205 residues, 1 model selected
> hide sel cartoons
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A,Bx,By,J,B,C,A9,7
3836 atoms, 4226 bonds, 207 residues, 1 model selected
> hide sel cartoons
> hide #!10 models
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #16/Ai #18/Ai
Alignment identifier is 1
> select #16/Ai:1-2 #18/Ai:1-2
26 atoms, 26 bonds, 4 residues, 2 models selected
> select #16/Ai #18/Ai
892 atoms, 908 bonds, 116 residues, 2 models selected
1 [ID: 1] region 2 chains [1-58] RMSD: 0.000
> blastprotein 1:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1
Webservices job id: W0XQ9DV70FJAPEAG
> select #16/Ai:1 #18/Ai:1
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #16/Ai:1-4 #18/Ai:1-4
60 atoms, 60 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [1-4] RMSD: 0.000
> select #16/Ai:1 #18/Ai:1
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #16/Ai #18/Ai
892 atoms, 908 bonds, 116 residues, 2 models selected
1 [ID: 1] region 2 chains [1-58] RMSD: 0.000
> save /home/miramay/Downloads/test_fasta format fasta alignment 1
Parsing BlastProtein results failed: HTTP Error 504: Gateway Time-out
> select
> #16/BU,B1,Bu,Bv,Bt,BV,j,BQ,BX,B2,BW,BS,Bz,B0,BZ,Ba,BO,Bp,Br,BT,BR,Bb,Bq,BN,Bs,BP,Bw,BY,B3,Bo,X,s,E,A,Bx,By,J,B,C,A9,7
3836 atoms, 4226 bonds, 207 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> select #16/Ap
592 atoms, 603 bonds, 77 residues, 1 model selected
> show #!2 models
> hide #!2 models
> open
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/cryosparc_P249_J460_003_volume_map_sharp.mrc
Opened cryosparc_P249_J460_003_volume_map_sharp.mrc as #19, grid size
440,440,440, pixel 1.06, shown at level 0.32, step 2, values float32
> volume #19 step 1
> surface dust #19 size 10.6
> view
> color #19 #b2b2b2ff models
> color #19 #b2b2b26e models
> hide #!19 models
> save
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/J460_modelangelo_EFG.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 184, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 656, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f2cca099590> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f29ea57b850>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 184, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 656, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f2cca099590> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f29ea57b850>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save
> /media/miramay/partition1/Backup/Projects/model_angelo_Mira/EFG/J460/J460_03142025/J460_model_angelo.cxs
> includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 184, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 656, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f2cca099590> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f29ea57b850>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/blastprotein/ui/results.py", line 184, in take_snapshot
"table_session": self.table.session_info(),
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 656, in session_info
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'selectedRows'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1051, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7f2cca099590> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7f29ea57b850>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f2cca099590> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7f29ea57b850>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.161.03
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D25
OS: Linux Mint 20.3
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
Cache Size: 25600 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 45Gi 5.3Gi 1.4Gi 11Gi 14Gi
Swap: 2.0Gi 2.0Gi 0B
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2504] (rev a1)
Subsystem: eVga.com. Corp. Device [3842:3652]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
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
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-Dicom: 1.2.6
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-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
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: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
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-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
fsspec: 2024.12.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
mpmath: 1.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
nvidia-cublas-cu12: 12.4.5.8
nvidia-cuda-cupti-cu12: 12.4.127
nvidia-cuda-nvrtc-cu12: 12.4.127
nvidia-cuda-runtime-cu12: 12.4.127
nvidia-cudnn-cu12: 9.1.0.70
nvidia-cufft-cu12: 11.2.1.3
nvidia-curand-cu12: 10.3.5.147
nvidia-cusolver-cu12: 11.6.1.9
nvidia-cusparse-cu12: 12.3.1.170
nvidia-nccl-cu12: 2.21.5
nvidia-nvjitlink-cu12: 12.4.127
nvidia-nvtx-cu12: 12.4.127
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
sympy: 1.13.1
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
torch: 2.5.1
tornado: 6.4.2
traitlets: 5.14.3
triton: 3.1.0
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session restore: ItemTable's selectionModel() is None (Parsing BlastProtein results failed) |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #16654