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Opened 3 years ago
Closed 3 years ago
#7553 closed defect (can't reproduce)
draw selection: glDrawBuffer: invalid operation
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1160.76.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /home/user3/Documents/ribosome_references_80S/40S_complete_figure.cxs
> format session
Opened 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 1.07, shown at level 0.85, step 1, values float32
Opened 3JAM_aligned_head_trial_zflipped_resampled4201.mrc as #1, grid size
420,420,420, pixel 1.07, shown at level 0.05, step 2, values float32
Log from Thu Sep 1 17:22:15 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /home/user3/Documents/ribosome_references_80S/40S_body_figure_final.cxs
Opened 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 1.07, shown at level 0.78, step 1, values float32
Log from Tue Aug 23 01:09:00 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure_colored.cxs
Log from Sat Aug 20 22:03:35 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/user3/Documents/ribosome_references_80S/80S_without_head/4v88.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/4v88.cif
---
warnings | Ignoring microheterogeneity for label_seq_id 3 in chain
Ignoring microheterogeneity for label_seq_id 4 in chain BO
Ignoring microheterogeneity for label_seq_id 11 in chain BO
Ignoring microheterogeneity for label_seq_id 13 in chain BO
Ignoring microheterogeneity for label_seq_id 16 in chain BO
35 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
G /A5:420
Atom OP2 has no neighbors to form bonds with according to residue template for
G /A5:420
4v88.cif title:
The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...]
Chain information for 4v88.cif #1
---
Chain | Description | UniProt
A1 A5 | 25S rRNA |
A2 | 18S ribosomal RNA |
A3 A7 | 5S rRNA |
A4 A8 | 5.8S rRNA |
A6 | 18S rRNA |
AA CA | 40S ribosomal protein S0-A | RSSA1_YEAST
AB CB | 40S ribosomal protein S1-A | RS3A1_YEAST
AC CC | 40S ribosomal protein S2 | RS2_YEAST
AD CD | 40S ribosomal protein S3 | RS3_YEAST
AE CE | 40S ribosomal protein S4-A | RS4A_YEAST
AF CF | 40S ribosomal protein S5 | RS5_YEAST
AG CG | 40S ribosomal protein S6-A | RS6A_YEAST
AH CH | 40S ribosomal protein S7-A | RS7A_YEAST
AI CI | 40S ribosomal protein S8-A | RS8A_YEAST
AJ CJ | 40S ribosomal protein S9-A | RS9A_YEAST
AK CK | 40S ribosomal protein S10-A | RS10A_YEAST
AL CL | 40S ribosomal protein S11-A | RS11A_YEAST
AM CM | 40S ribosomal protein S12 | RS12_YEAST
AN CN | 40S ribosomal protein S13 | RS13_YEAST
AO CO | 40S ribosomal protein S14-A | RS14A_YEAST
AP CP | 40S ribosomal protein S15 | RS15_YEAST
AQ CQ | 40S ribosomal protein S16-A | RS16A_YEAST
AR CR | 40S ribosomal protein S17-A | RS17A_YEAST
AS CS | 40S ribosomal protein S18-A | RS18A_YEAST
AT CT | 40S ribosomal protein S19-A | RS19A_YEAST
AU CU | 40S ribosomal protein S20 | RS20_YEAST
AV CV | 40S ribosomal protein S21-A | RS21A_YEAST
AW CW | 40S ribosomal protein S22-A | RS22A_YEAST
AX CX | 40S ribosomal protein S23-A | RS23A_YEAST
AY CY | 40S ribosomal protein S24-A | RS24A_YEAST
AZ CZ | 40S ribosomal protein S25-A | RS25A_YEAST
Aa Ca | 40S ribosomal protein S26-A | RS26A_YEAST
Ab Cb | 40S ribosomal protein S27-A | RS27_YEAST
Ac Cc | 40S ribosomal protein S28-A | RS28A_YEAST
Ad Cd | 40S ribosomal protein S29-A | RS29A_YEAST
Ae Ce | 40S ribosomal protein S30-A | RS30A_YEAST
Af Cf | 40S ribosomal protein S31 | RS27A_YEAST
Ag Cg | Guanine nucleotide-binding protein subunit beta-like protein (ASC1,
RACK1) | GBLP_YEAST
Ah | Suppressor protein STM1 | STM1_YEAST
BA DA | 60S ribosomal protein L2-A | RL2A_YEAST
BB DB | 60S ribosomal protein L3 | RL3_YEAST
BC DC | 60S ribosomal protein L4-A | RL4A_YEAST
BD DD | 60S ribosomal protein L5 | RL5_YEAST
BE DE | 60S ribosomal protein L6-A | RL6A_YEAST
BF DF | 60S ribosomal protein L7-A | RL7A_YEAST
BG DG | 60S ribosomal protein L8-A | RL8A_YEAST
BH DH | 60S ribosomal protein L9-A | RL9A_YEAST
BI DI | 60S ribosomal protein L10 | RL10_YEAST
BJ DJ | 60S ribosomal protein L11-A | RL11A_YEAST
BL DL | 60S ribosomal protein L13-A | RL13A_YEAST
BM DM | 60S ribosomal protein L14-A | RL14A_YEAST
BN DN | 60S ribosomal protein L15-A | RL15A_YEAST
BO DO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B | RL16A_YEAST
BP DP | 60S ribosomal protein L17-A | RL17A_YEAST
BQ DQ | 60S ribosomal protein L18-A | RL18A_YEAST
BR DR | 60S ribosomal protein L19-A | RL19A_YEAST
BS DS | 60S ribosomal protein L20-A | RL20A_YEAST
BT DT | 60S ribosomal protein L21-A | RL21A_YEAST
BU DU | 60S ribosomal protein L22-A | RL22A_YEAST
BV DV | 60S ribosomal protein L23-A | RL23A_YEAST
BW DW | 60S ribosomal protein L24-A | RL24A_YEAST
BX DX | 60S ribosomal protein L25 | RL25_YEAST
BY DY | 60S ribosomal protein L26-A | RL26A_YEAST
BZ DZ | 60S ribosomal protein L27-A | RL27A_YEAST
Ba Da | 60S ribosomal protein L28 | RL28_YEAST
Bb Db | 60S ribosomal protein L29 | RL29_YEAST
Bc Dc | 60S ribosomal protein L30 | RL30_YEAST
Bd Dd | 60S ribosomal protein L31-A | RL31A_YEAST
Be De | 60S ribosomal protein L32 | RL32_YEAST
Bf Df | 60S ribosomal protein L33-A | RL33A_YEAST
Bg Dg | 60S ribosomal protein L34-A | RL34A_YEAST
Bh Dh | 60S ribosomal protein L35-A | RL35A_YEAST
Bi Di | 60S ribosomal protein L36-A | RL36A_YEAST
Bj Dj | 60S ribosomal protein L37-A | RL37A_YEAST
Bk Dk | 60S ribosomal protein L38 | RL38_YEAST
Bl Dl | 60S ribosomal protein L39 | RL39_YEAST
Bm Dm | 60S ribosomal protein L40 | RL401_YEAST
Bn Dn | 60S ribosomal protein L41-A | RL41A_YEAST
Bo Do | 60S ribosomal protein L42-A | RL44A_YEAST
Bp Dp | 60S ribosomal protein L43-A | RL34A_YEAST,RL43A_YEAST
Ch | Suppressor protein STM1 | RLA0_YEAST
DK | Ribosomal protein L12 |
Dq | 60S acidic ribosomal protein P0 | RLA0_YEAST
Dr | Ribosomal protein P1 α |
Ds | Ribosomal protein P2 β |
Non-standard residues in 4v88.cif #1
---
MG — magnesium ion
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)
ZN — zinc ion
4v88.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> show cartoons
> show atoms
> hide atoms
> select /AT:63
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
134 atoms, 139 bonds, 15 residues, 1 model selected
> select up
1112 atoms, 1130 bonds, 143 residues, 1 model selected
> select up
413613 atoms, 431464 bonds, 36905 residues, 1 model selected
> select down
1112 atoms, 1130 bonds, 143 residues, 1 model selected
Drag select of 11657 residues, 7 pseudobonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 5162 residues, 82 pseudobonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 3 pseudobonds
No visible atoms or bonds selected
> select /DK:33
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 6 residues, 1 model selected
> select up
750 atoms, 747 bonds, 150 residues, 1 model selected
> select up
209852 atoms, 212653 bonds, 20086 residues, 1 model selected
> select down
750 atoms, 747 bonds, 150 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 7617 residues, 26 pseudobonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /A5:1026
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
14123 atoms, 15759 bonds, 660 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 48 residues, 3 pseudobonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 100 residues, 8 pseudobonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> lighting soft
> select /DZ:106
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
179 atoms, 181 bonds, 21 residues, 1 model selected
> select up
1046 atoms, 1070 bonds, 129 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/yeast_4v88_body.pdb
> relModel #1
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/yeast_4v88_body.pdb
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/yeast_4v88_body.pdb
---
warnings | Cannot find LINK/SSBOND residue A (2813 )
Cannot find LINK/SSBOND residue G (16 )
Cannot find LINK/SSBOND residue C (17 )
Cannot find LINK/SSBOND residue A (28 )
Cannot find LINK/SSBOND residue C (36 )
229 messages similar to the above omitted
Chain information for yeast_4v88_body.pdb #2
---
Chain | Description
A1 | No description available
A6 | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CK | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
CZ | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Cf | No description available
Cg | No description available
Ch | No description available
DA | No description available
DB | No description available
DC | No description available
DG | No description available
DJ | No description available
DR | No description available
DV | No description available
DW | No description available
Dc | No description available
Dg | No description available
Dn | No description available
Do | No description available
Dp | No description available
> hide #!1 models
> hide #!1 target m
> select clear
[Repeated 1 time(s)]
> select #2/A2:2012@N4
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 1 residue, 1 model selected
> select up
1487 atoms, 359 residues, 1 model selected
> select up
96665 atoms, 90232 bonds, 11382 residues, 1 model selected
> select down
1487 atoms, 359 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A1:3611@N5
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 1 residue, 1 model selected
> select up
3673 atoms, 94 bonds, 1112 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A3:201@N2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 1 residue, 1 model selected
> select up
110 atoms, 32 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A5:3640@N2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 1 residue, 1 model selected
> select up
3689 atoms, 1181 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 732 atoms, 379 pseudobonds, 70 bonds
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
Drag select of 246 atoms, 142 pseudobonds, 7 bonds
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
Drag select of 26 atoms, 16 pseudobonds
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/DI:301@N4
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 1 residue, 1 model selected
> select up
21 atoms, 8 bonds, 3 residues, 1 model selected
> select up
86702 atoms, 90051 bonds, 8322 residues, 1 model selected
> select down
21 atoms, 8 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A7:213@N1
1 atom, 1 residue, 1 model selected
> select #2/DH:201@N4
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A7:213@N6
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A7:213@N4
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 cartoons
> hide #!2 atoms
> select #2
86667 atoms, 90043 bonds, 1574 pseudobonds, 8317 residues, 3 models selected
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/yeast_4v88_body.pdb
> models #2 selectedOnly true
> close #1
> select clear
> open /home/user3/Documents/ribosome_references_80S/80S_without_head/7qix.pdb
7qix.pdb title:
Specific features and methylation sites of A plant ribosome. 40S body
ribosomal subunit. [more info...]
Chain information for 7qix.pdb #1
---
Chain | Description | UniProt
2 | 18S RRNA body |
D | 60S ribosomal protein L41 | K4C3A4_SOLLC
E | 40S ribosomal protein sa |
F | 40S ribosomal protein S3A |
G | 40S body ribosomal protein ES4 |
H | 40S ribosomal protein S7 |
I | 40S ribosomal protein S8 |
J | ribosomal_S17_N domain-containing protein | K4C998_SOLLC
K | 40S ribosomal protein S17 | RS17_SOLLC
L | 40S ribosomal protein S21 |
M | 40S body ribosomal protein US12 | K4D3L7_SOLLC
N | 40S ribosomal protein S26 |
O | S5 DRBM domain-containing protein |
P | 40S ribosomal protein S6 |
Q | 40S body ribosomal protein US4 | K4ATQ2_SOLLC
R | 30S ribosomal protein S15, chloroplastic | K4CYU9_SOLLC
S | ribosomal protein S14-LIKE | Q38JI8_SOLTU
T | 40S ribosomal protein S15A-1 isoform X1 |
U | 40S ribosomal protein S24 |
V | 40S ribosomal protein S27 |
W | 40S ribosomal protein S30 |
X | ribosomal protein L19 |
Non-standard residues in 7qix.pdb #1
---
4AC — N(4)-acetylcytidine-5'-monophosphate
6MZ — N6-methyladenosine-5'-monophosphate
A2M — 2'-O-methyladenosine 5'-(dihydrogen phosphate)
IAS — β-L-aspartic acid (L-aspartic acid)
K — potassium ion
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
OMC — O2'-methylycytidine-5'-monophosphate
OMG — O2'-methylguanosine-5'-monophosphate
OMU — O2'-methyluridine 5'-monophosphate
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
> show cartoons
> hide atoms
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7qix.pdb, chain G (#1) with yeast_4v88_body.pdb, chain CE (#2),
sequence alignment score = 852.9
RMSD between 252 pruned atom pairs is 0.565 angstroms; (across all 260 pairs:
0.764)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7qix.pdb, chain G (#1) with yeast_4v88_body.pdb, chain CE (#2),
sequence alignment score = 852.9
RMSD between 252 pruned atom pairs is 0.565 angstroms; (across all 260 pairs:
0.764)
> color #1 #ef2929 transparency 0
> color #2 #fce94f transparency 0
> select #2/DR:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
202 atoms, 205 bonds, 23 residues, 1 model selected
> select up
1078 atoms, 1090 bonds, 131 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/Dg:69
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 4 residues, 1 model selected
> select up
492 atoms, 485 bonds, 67 residues, 1 model selected
> select up
85589 atoms, 88953 bonds, 8186 residues, 1 model selected
> select down
492 atoms, 485 bonds, 67 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/DA:60
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
85 atoms, 86 bonds, 11 residues, 1 model selected
> select up
1517 atoms, 1529 bonds, 202 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/Dc:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
92 atoms, 92 bonds, 12 residues, 1 model selected
> select up
767 atoms, 775 bonds, 100 residues, 1 model selected
> select up
83580 atoms, 86939 bonds, 7917 residues, 1 model selected
> select down
767 atoms, 775 bonds, 100 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/Dp:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 5 residues, 1 model selected
> select up
698 atoms, 701 bonds, 95 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/DB:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
41 atoms, 40 bonds, 5 residues, 1 model selected
> select up
547 atoms, 537 bonds, 74 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/DV:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
42 atoms, 44 bonds, 4 residues, 1 model selected
> select up
994 atoms, 998 bonds, 138 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/DW:48
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 5 residues, 1 model selected
> select up
1039 atoms, 1052 bonds, 136 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_1_after_real_space_refined_real_space_refined_018.pdb
Chain information for
40S_1_after_real_space_refined_real_space_refined_018.pdb #3
---
Chain | Description
Ad | No description available
BA | No description available
BB | No description available
BC | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BL | No description available
BN | No description available
BO | No description available
BR | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
Ba | No description available
Bb | No description available
Be | No description available
Cn | No description available
> show cartoons
> hide atoms
> color #3 #e9b96e transparency 0
> color #3 #8ae234 transparency 0
> color #3 #729fcf transparency 0
> ui tool show Matchmaker
> matchmaker #!1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BG
(#3) with 7qix.pdb, chain P (#1), sequence alignment score = 1038.1
RMSD between 210 pruned atom pairs is 0.800 angstroms; (across all 229 pairs:
1.169)
> matchmaker #!1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BG
(#3) with 7qix.pdb, chain P (#1), sequence alignment score = 1038.1
RMSD between 210 pruned atom pairs is 0.800 angstroms; (across all 229 pairs:
1.169)
> ui tool show Matchmaker
> matchmaker #!3 to #1 bring #!2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7qix.pdb, chain P (#1) with
40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BG (#3),
sequence alignment score = 1038.1
RMSD between 210 pruned atom pairs is 0.800 angstroms; (across all 229 pairs:
1.169)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7qix.pdb, chain G (#1) with yeast_4v88_body.pdb, chain CE (#2),
sequence alignment score = 852.9
RMSD between 252 pruned atom pairs is 0.565 angstroms; (across all 260 pairs:
0.764)
> select #2/DG:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
59 atoms, 58 bonds, 9 residues, 1 model selected
> select up
198 atoms, 200 bonds, 28 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/X:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
533 atoms, 534 bonds, 30 residues, 1 model selected
> select up
570 atoms, 571 bonds, 32 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/A6:716
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
37999 atoms, 42488 bonds, 1795 residues, 1 model selected
> select up
39637 atoms, 42488 bonds, 2234 residues, 1 model selected
> select clear
> select #2/A6:656
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> style sel stick
Changed 23 atom styles
> style sel stick
Changed 23 atom styles
> style sel stick
Changed 23 atom styles
> hide sel cartoons
> show sel cartoons
> select #2/CY:134
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
110 atoms, 109 bonds, 14 residues, 1 model selected
> select up
1089 atoms, 1087 bonds, 138 residues, 1 model selected
> select clear
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> open /home/user3/Documents/ribosome_references_80S/80S_without_head/6qzp.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/6qzp.cif
---
notes | Fetching CCD HMT from http://ligand-
expo.rcsb.org/reports/H/HMT/HMT.cif
Fetching CCD HYG from http://ligand-expo.rcsb.org/reports/H/HYG/HYG.cif
Fetching CCD 2MG from http://ligand-expo.rcsb.org/reports/2/2MG/2MG.cif
Fetching CCD JMH from http://ligand-expo.rcsb.org/reports/J/JMH/JMH.cif
Fetching CCD B8H from http://ligand-expo.rcsb.org/reports/B/B8H/B8H.cif
Fetching CCD B8T from http://ligand-expo.rcsb.org/reports/B/B8T/B8T.cif
Fetching CCD M7A from http://ligand-expo.rcsb.org/reports/M/M7A/M7A.cif
6qzp.cif title:
High-resolution cryo-EM structure of the human 80S ribosome [more info...]
Chain information for 6qzp.cif #4
---
Chain | Description | UniProt
L5 | 28S rRNA (3773-MER) |
L7 | 5S rRNA (120-MER) |
L8 | 5.8S rRNA (156-MER) |
LA | 60S ribosomal protein L8 | RL8_HUMAN
LB | 60S ribosomal protein L3 | RL3_HUMAN
LC | 60S ribosomal protein L4 | RL4_HUMAN
LD | 60S ribosomal protein L5 | RL5_HUMAN
LE | 60S ribosomal protein L6 | RL6_HUMAN
LF | 60S ribosomal protein L7 | RL7_HUMAN
LG | 60S ribosomal protein L7a | RL7A_HUMAN
LH | 60S ribosomal protein L9 | RL9_HUMAN
LI | 60S ribosomal protein L10-like | RL10L_HUMAN
LJ | 60S ribosomal protein L11 | RL11_HUMAN
LL | 60S ribosomal protein L13 | RL13_HUMAN
LM | 60S ribosomal protein L14 | RL14_HUMAN
LN | 60S ribosomal protein L15 | RL15_HUMAN
LO | 60S ribosomal protein L13a | RL13A_HUMAN
LP | 60S ribosomal protein L17 | RL17_HUMAN
LQ | 60S ribosomal protein L18 | RL18_HUMAN
LR | 60S ribosomal protein L19 | RL19_HUMAN
LS | 60S ribosomal protein L18a | RL18A_HUMAN
LT | 60S ribosomal protein L21 | RL21_HUMAN
LU | 60S ribosomal protein L22 | RL22_HUMAN
LV | 60S ribosomal protein L23 | RL23_HUMAN
LW | 60S ribosomal protein L24 | RL24_HUMAN
LX | 60S ribosomal protein L23a | RL23A_HUMAN
LY | 60S ribosomal protein L26 | RL26_HUMAN
LZ | 60S ribosomal protein L27 | RL27_HUMAN
La | 60S ribosomal protein L27a | RL27A_HUMAN
Lb | 60S ribosomal protein L29 | RL29_HUMAN
Lc | 60S ribosomal protein L30 | RL30_HUMAN
Ld | 60S ribosomal protein L31 | RL31_HUMAN
Le | 60S ribosomal protein L32 | RL32_HUMAN
Lf | 60S ribosomal protein L35a | RL35A_HUMAN
Lg | 60S ribosomal protein L34 | RL34_HUMAN
Lh | 60S ribosomal protein L35 | RL35_HUMAN
Li | 60S ribosomal protein L36 | RL36_HUMAN
Lj | 60S ribosomal protein L37 | RL37_HUMAN
Lk | 60S ribosomal protein L38 | RL38_HUMAN
Ll | 60S ribosomal protein L39 | RL39_HUMAN
Lm | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN
Ln | 60S ribosomal protein L41 | RL41_HUMAN
Lo | 60S ribosomal protein L36a | RL36A_HUMAN
Lp | 60S ribosomal protein L37a | RL37A_HUMAN
Lr | 60S ribosomal protein L28 | RL28_HUMAN
Lz | 60S ribosomal protein L10a | RL10A_HUMAN
S2 | 18S rRNA (1740-MER) |
S6 | E site tRNA (75-MER) |
SA | 40S ribosomal protein SA | RSSA_HUMAN
SB | 40S ribosomal protein S3a | RS3A_HUMAN
SC | 40S ribosomal protein S2 | RS2_HUMAN
SD | 40S ribosomal protein S3 | RS3_HUMAN
SE | 40S ribosomal protein S4, X isoform | RS4X_HUMAN
SF | 40S ribosomal protein S5 | RS5_HUMAN
SG | 40S ribosomal protein S6 | RS6_HUMAN
SH | 40S ribosomal protein S7 | RS7_HUMAN
SI | 40S ribosomal protein S8 | RS8_HUMAN
SJ | 40S ribosomal protein S9 | RS9_HUMAN
SK | 40S ribosomal protein S10 | RS10_HUMAN
SL | 40S ribosomal protein S11 | RS11_HUMAN
SM | 40S ribosomal protein S12 | RS12_HUMAN
SN | 40S ribosomal protein S13 | RS13_HUMAN
SO | 40S ribosomal protein S14 | RS14_HUMAN
SP | 40S ribosomal protein S15 | RS15_HUMAN
SQ | 40S ribosomal protein S16 | RS16_HUMAN
SR | 40S ribosomal protein S17 | RS17_HUMAN
SS | 40S ribosomal protein S18 | RS18_HUMAN
ST | 40S ribosomal protein S19 | RS19_HUMAN
SU | 40S ribosomal protein S20 | RS20_HUMAN
SV | 40S ribosomal protein S21 | RS21_HUMAN
SW | 40S ribosomal protein S15a | RS15A_HUMAN
SX | 40S ribosomal protein S23 | RS23_HUMAN
SY | 40S ribosomal protein S24 | RS24_HUMAN
SZ | 40S ribosomal protein S25 | RS25_HUMAN
Sa | 40S ribosomal protein S26 | RS26_HUMAN
Sb | 40S ribosomal protein S27 | RS27_HUMAN
Sc | 40S ribosomal protein S28 | RS28_HUMAN
Sd | 40S ribosomal protein S29 | RS29_HUMAN
Se | 40S ribosomal protein S30 | RS30_HUMAN
Sf | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN
Sg | Receptor of activated protein C kinase 1 | RACK1_HUMAN
Non-standard residues in 6qzp.cif #4
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
HMT —
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
(Homoharringtonine; Cephalotaxine; [3(R)]-4-methyl
2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate)
HYG — hygromycin B (hygromix; antihelmycin; hydromycin B; destomysin;
antibiotic A-396-II)
MG — magnesium ion
ZN — zinc ion
> show #!4 cartoons
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8 atoms, 7 bonds, 1 residue, 1 model selected
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24 atoms, 23 bonds, 4 residues, 1 model selected
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224 atoms, 223 bonds, 31 residues, 1 model selected
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7 atoms, 7 bonds, 1 residue, 1 model selected
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114 atoms, 114 bonds, 14 residues, 1 model selected
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1050 atoms, 1072 bonds, 127 residues, 1 model selected
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20 atoms, 21 bonds, 1 residue, 1 model selected
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36938 atoms, 41288 bonds, 1740 residues, 1 model selected
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9 atoms, 8 bonds, 1 residue, 1 model selected
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26 atoms, 25 bonds, 3 residues, 1 model selected
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1074 atoms, 1085 bonds, 126 residues, 1 model selected
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228 atoms, 228 bonds, 28 residues, 1 model selected
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458 atoms, 460 bonds, 61 residues, 1 model selected
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> show #!2 models
> ui tool show Matchmaker
> matchmaker #!1-3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6qzp.cif, chain SE (#4) with 7qix.pdb, chain G (#1), sequence
alignment score = 912.6
RMSD between 257 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
0.629)
Matchmaker 6qzp.cif, chain SE (#4) with yeast_4v88_body.pdb, chain CE (#2),
sequence alignment score = 945.7
RMSD between 256 pruned atom pairs is 0.574 angstroms; (across all 260 pairs:
0.669)
Matchmaker 6qzp.cif, chain SE (#4) with
40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BE (#3),
sequence alignment score = 814.1
RMSD between 227 pruned atom pairs is 0.966 angstroms; (across all 261 pairs:
1.711)
> matchmaker #!1-3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6qzp.cif, chain SE (#4) with 7qix.pdb, chain G (#1), sequence
alignment score = 912.6
RMSD between 257 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
0.629)
Matchmaker 6qzp.cif, chain SE (#4) with yeast_4v88_body.pdb, chain CE (#2),
sequence alignment score = 945.7
RMSD between 256 pruned atom pairs is 0.574 angstroms; (across all 260 pairs:
0.669)
Matchmaker 6qzp.cif, chain SE (#4) with
40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BE (#3),
sequence alignment score = 814.1
RMSD between 227 pruned atom pairs is 0.966 angstroms; (across all 261 pairs:
1.711)
> matchmaker #!1-3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6qzp.cif, chain SE (#4) with 7qix.pdb, chain G (#1), sequence
alignment score = 912.6
RMSD between 257 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
0.629)
Matchmaker 6qzp.cif, chain SE (#4) with yeast_4v88_body.pdb, chain CE (#2),
sequence alignment score = 945.7
RMSD between 256 pruned atom pairs is 0.574 angstroms; (across all 260 pairs:
0.669)
Matchmaker 6qzp.cif, chain SE (#4) with
40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BE (#3),
sequence alignment score = 814.1
RMSD between 227 pruned atom pairs is 0.966 angstroms; (across all 261 pairs:
1.711)
> color #4 #5c3566 transparency 0
> show #!3 models
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81860 atoms, 86506 bonds, 1643 pseudobonds, 7765 residues, 4 models selected
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/human_body_6qzp.pdb
> models #4 selectedOnly true
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7 atoms, 6 bonds, 1 residue, 1 model selected
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35 atoms, 34 bonds, 5 residues, 1 model selected
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822 atoms, 828 bonds, 112 residues, 1 model selected
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8 atoms, 7 bonds, 1 residue, 1 model selected
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52 atoms, 51 bonds, 7 residues, 1 model selected
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96 atoms, 95 bonds, 14 residues, 1 model selected
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5862 atoms, 5904 bonds, 1 pseudobond, 479 residues, 3 models selected
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298 atoms, 299 bonds, 36 residues, 1 model selected
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1849 atoms, 1871 bonds, 229 residues, 1 model selected
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1367 atoms, 1263 bonds, 210 residues, 4 models selected
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11 atoms, 10 bonds, 1 residue, 1 model selected
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47 atoms, 46 bonds, 5 residues, 1 model selected
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1849 atoms, 1871 bonds, 229 residues, 1 model selected
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1367 atoms, 1263 bonds, 210 residues, 4 models selected
> select sequence BG
1367 atoms, 1263 bonds, 210 residues, 4 models selected
> select sequence BG
1367 atoms, 1263 bonds, 210 residues, 4 models selected
> select sequence BG
1367 atoms, 1263 bonds, 210 residues, 4 models selected
> select sequence BG
1367 atoms, 1263 bonds, 210 residues, 4 models selected
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83527 atoms, 86093 bonds, 384 pseudobonds, 4640 residues, 3 models selected
> ~select #1
Nothing selected
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11 atoms, 10 bonds, 1 residue, 1 model selected
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1849 atoms, 1871 bonds, 229 residues, 1 model selected
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1367 atoms, 1263 bonds, 210 residues, 4 models selected
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47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> ~select #3
Nothing selected
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47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> select sequence BG
1367 atoms, 1263 bonds, 210 residues, 4 models selected
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83527 atoms, 86093 bonds, 384 pseudobonds, 4640 residues, 3 models selected
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Nothing selected
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9 atoms, 8 bonds, 1 residue, 1 model selected
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131 atoms, 131 bonds, 17 residues, 1 model selected
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709 atoms, 718 bonds, 92 residues, 1 model selected
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122 atoms, 124 bonds, 15 residues, 1 model selected
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764 atoms, 774 bonds, 98 residues, 1 model selected
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65 atoms, 66 bonds, 8 residues, 1 model selected
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1049 atoms, 1057 bonds, 143 residues, 1 model selected
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9 atoms, 8 bonds, 1 residue, 1 model selected
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110 atoms, 110 bonds, 14 residues, 1 model selected
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1741 atoms, 1778 bonds, 221 residues, 1 model selected
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8 atoms, 7 bonds, 1 residue, 1 model selected
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139 atoms, 144 bonds, 17 residues, 1 model selected
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1554 atoms, 1588 bonds, 195 residues, 1 model selected
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> open /home/user3/Documents/ribosome_references_80S/80S_without_head/4v88.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/4v88.cif
---
warnings | Ignoring microheterogeneity for label_seq_id 3 in chain
Ignoring microheterogeneity for label_seq_id 4 in chain BO
Ignoring microheterogeneity for label_seq_id 11 in chain BO
Ignoring microheterogeneity for label_seq_id 13 in chain BO
Ignoring microheterogeneity for label_seq_id 16 in chain BO
35 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
G /A5:420
Atom OP2 has no neighbors to form bonds with according to residue template for
G /A5:420
4v88.cif title:
The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...]
Chain information for 4v88.cif #5
---
Chain | Description | UniProt
A1 A5 | 25S rRNA |
A2 | 18S ribosomal RNA |
A3 A7 | 5S rRNA |
A4 A8 | 5.8S rRNA |
A6 | 18S rRNA |
AA CA | 40S ribosomal protein S0-A | RSSA1_YEAST
AB CB | 40S ribosomal protein S1-A | RS3A1_YEAST
AC CC | 40S ribosomal protein S2 | RS2_YEAST
AD CD | 40S ribosomal protein S3 | RS3_YEAST
AE CE | 40S ribosomal protein S4-A | RS4A_YEAST
AF CF | 40S ribosomal protein S5 | RS5_YEAST
AG CG | 40S ribosomal protein S6-A | RS6A_YEAST
AH CH | 40S ribosomal protein S7-A | RS7A_YEAST
AI CI | 40S ribosomal protein S8-A | RS8A_YEAST
AJ CJ | 40S ribosomal protein S9-A | RS9A_YEAST
AK CK | 40S ribosomal protein S10-A | RS10A_YEAST
AL CL | 40S ribosomal protein S11-A | RS11A_YEAST
AM CM | 40S ribosomal protein S12 | RS12_YEAST
AN CN | 40S ribosomal protein S13 | RS13_YEAST
AO CO | 40S ribosomal protein S14-A | RS14A_YEAST
AP CP | 40S ribosomal protein S15 | RS15_YEAST
AQ CQ | 40S ribosomal protein S16-A | RS16A_YEAST
AR CR | 40S ribosomal protein S17-A | RS17A_YEAST
AS CS | 40S ribosomal protein S18-A | RS18A_YEAST
AT CT | 40S ribosomal protein S19-A | RS19A_YEAST
AU CU | 40S ribosomal protein S20 | RS20_YEAST
AV CV | 40S ribosomal protein S21-A | RS21A_YEAST
AW CW | 40S ribosomal protein S22-A | RS22A_YEAST
AX CX | 40S ribosomal protein S23-A | RS23A_YEAST
AY CY | 40S ribosomal protein S24-A | RS24A_YEAST
AZ CZ | 40S ribosomal protein S25-A | RS25A_YEAST
Aa Ca | 40S ribosomal protein S26-A | RS26A_YEAST
Ab Cb | 40S ribosomal protein S27-A | RS27_YEAST
Ac Cc | 40S ribosomal protein S28-A | RS28A_YEAST
Ad Cd | 40S ribosomal protein S29-A | RS29A_YEAST
Ae Ce | 40S ribosomal protein S30-A | RS30A_YEAST
Af Cf | 40S ribosomal protein S31 | RS27A_YEAST
Ag Cg | Guanine nucleotide-binding protein subunit beta-like protein (ASC1,
RACK1) | GBLP_YEAST
Ah | Suppressor protein STM1 | STM1_YEAST
BA DA | 60S ribosomal protein L2-A | RL2A_YEAST
BB DB | 60S ribosomal protein L3 | RL3_YEAST
BC DC | 60S ribosomal protein L4-A | RL4A_YEAST
BD DD | 60S ribosomal protein L5 | RL5_YEAST
BE DE | 60S ribosomal protein L6-A | RL6A_YEAST
BF DF | 60S ribosomal protein L7-A | RL7A_YEAST
BG DG | 60S ribosomal protein L8-A | RL8A_YEAST
BH DH | 60S ribosomal protein L9-A | RL9A_YEAST
BI DI | 60S ribosomal protein L10 | RL10_YEAST
BJ DJ | 60S ribosomal protein L11-A | RL11A_YEAST
BL DL | 60S ribosomal protein L13-A | RL13A_YEAST
BM DM | 60S ribosomal protein L14-A | RL14A_YEAST
BN DN | 60S ribosomal protein L15-A | RL15A_YEAST
BO DO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B | RL16A_YEAST
BP DP | 60S ribosomal protein L17-A | RL17A_YEAST
BQ DQ | 60S ribosomal protein L18-A | RL18A_YEAST
BR DR | 60S ribosomal protein L19-A | RL19A_YEAST
BS DS | 60S ribosomal protein L20-A | RL20A_YEAST
BT DT | 60S ribosomal protein L21-A | RL21A_YEAST
BU DU | 60S ribosomal protein L22-A | RL22A_YEAST
BV DV | 60S ribosomal protein L23-A | RL23A_YEAST
BW DW | 60S ribosomal protein L24-A | RL24A_YEAST
BX DX | 60S ribosomal protein L25 | RL25_YEAST
BY DY | 60S ribosomal protein L26-A | RL26A_YEAST
BZ DZ | 60S ribosomal protein L27-A | RL27A_YEAST
Ba Da | 60S ribosomal protein L28 | RL28_YEAST
Bb Db | 60S ribosomal protein L29 | RL29_YEAST
Bc Dc | 60S ribosomal protein L30 | RL30_YEAST
Bd Dd | 60S ribosomal protein L31-A | RL31A_YEAST
Be De | 60S ribosomal protein L32 | RL32_YEAST
Bf Df | 60S ribosomal protein L33-A | RL33A_YEAST
Bg Dg | 60S ribosomal protein L34-A | RL34A_YEAST
Bh Dh | 60S ribosomal protein L35-A | RL35A_YEAST
Bi Di | 60S ribosomal protein L36-A | RL36A_YEAST
Bj Dj | 60S ribosomal protein L37-A | RL37A_YEAST
Bk Dk | 60S ribosomal protein L38 | RL38_YEAST
Bl Dl | 60S ribosomal protein L39 | RL39_YEAST
Bm Dm | 60S ribosomal protein L40 | RL401_YEAST
Bn Dn | 60S ribosomal protein L41-A | RL41A_YEAST
Bo Do | 60S ribosomal protein L42-A | RL44A_YEAST
Bp Dp | 60S ribosomal protein L43-A | RL34A_YEAST,RL43A_YEAST
Ch | Suppressor protein STM1 | RLA0_YEAST
DK | Ribosomal protein L12 |
Dq | 60S acidic ribosomal protein P0 | RLA0_YEAST
Dr | Ribosomal protein P1 α |
Ds | Ribosomal protein P2 β |
Non-standard residues in 4v88.cif #5
---
MG — magnesium ion
OHX — osmium (III) hexammine (osmium(6+) hexaazanide)
ZN — zinc ion
4v88.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> show #!2-3,5 cartoons
> hide #!2-3,5 atoms
> ui tool show Matchmaker
> matchmaker #!1-4 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4v88.cif, chain AE (#5) with 7qix.pdb, chain G (#1), sequence
alignment score = 868.5
RMSD between 253 pruned atom pairs is 0.611 angstroms; (across all 260 pairs:
0.842)
Matchmaker 4v88.cif, chain Cg (#5) with yeast_4v88_body.pdb, chain Cg (#2),
sequence alignment score = 1643.8
RMSD between 318 pruned atom pairs is 0.000 angstroms; (across all 318 pairs:
0.000)
Matchmaker 4v88.cif, chain CC (#5) with
40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BC (#3),
sequence alignment score = 803.8
RMSD between 204 pruned atom pairs is 0.795 angstroms; (across all 217 pairs:
1.111)
Matchmaker 4v88.cif, chain CE (#5) with 6qzp.cif, chain SE (#4), sequence
alignment score = 945.7
RMSD between 256 pruned atom pairs is 0.574 angstroms; (across all 260 pairs:
0.669)
> matchmaker #!1-4 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4v88.cif, chain AE (#5) with 7qix.pdb, chain G (#1), sequence
alignment score = 868.5
RMSD between 253 pruned atom pairs is 0.611 angstroms; (across all 260 pairs:
0.842)
Matchmaker 4v88.cif, chain Cg (#5) with yeast_4v88_body.pdb, chain Cg (#2),
sequence alignment score = 1643.8
RMSD between 318 pruned atom pairs is 0.000 angstroms; (across all 318 pairs:
0.000)
Matchmaker 4v88.cif, chain CC (#5) with
40S_1_after_real_space_refined_real_space_refined_018.pdb, chain BC (#3),
sequence alignment score = 803.8
RMSD between 204 pruned atom pairs is 0.795 angstroms; (across all 217 pairs:
1.111)
Matchmaker 4v88.cif, chain CE (#5) with 6qzp.cif, chain SE (#4), sequence
alignment score = 945.7
RMSD between 256 pruned atom pairs is 0.574 angstroms; (across all 260 pairs:
0.669)
> hide #!2 models
> color #3 #f57900 transparency 0
> color #5 #8ae234 transparency 0
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> select #4
77419 atoms, 82020 bonds, 1628 pseudobonds, 7184 residues, 4 models selected
> save /home/user3/Documents/ribosome_references_80S/80S_without_head/6qzp.cif
> models #4 selectedOnly true relModel #3
> ~select #4
Nothing selected
> hide #!5 models
> show #!2 models
> hide #!4 models
> close #5
> close #4
> close #2
> close #1
> select /BG:215
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /Ad:126
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select /BA
1554 atoms, 1588 bonds, 195 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> color sel gold
> select /BB
1728 atoms, 1758 bonds, 213 residues, 1 model selected
> select /BB
1728 atoms, 1758 bonds, 213 residues, 1 model selected
> color sel coral
> ui tool show "Color Actions"
> color sel coral
> select /BC
1707 atoms, 1744 bonds, 220 residues, 1 model selected
> color sel lavender blush
> select /BE
2083 atoms, 2122 bonds, 263 residues, 1 model selected
> color sel sea green
> select /BG
1849 atoms, 1871 bonds, 229 residues, 1 model selected
> color sel indigo
> select /BH
1373 atoms, 1399 bonds, 182 residues, 1 model selected
> color sel green yellow
> select /BI
1499 atoms, 1522 bonds, 1 pseudobond, 186 residues, 2 models selected
> color sel medium orchid
> select /BC
1707 atoms, 1744 bonds, 220 residues, 1 model selected
> color sel ivory
[Repeated 1 time(s)]
> select /BJ
1513 atoms, 1542 bonds, 183 residues, 1 model selected
> color sel honeydew
> color sel cadet blue
> color sel gold
> select /BA
1554 atoms, 1588 bonds, 195 residues, 1 model selected
> color sel cadet blue
> select /BL
1200 atoms, 1227 bonds, 151 residues, 1 model selected
> select /BL
1200 atoms, 1227 bonds, 151 residues, 1 model selected
> color sel antique white
> select /BN
1188 atoms, 1212 bonds, 149 residues, 1 model selected
> color sel medium purple
> select /BO
983 atoms, 995 bonds, 130 residues, 1 model selected
> color sel brown
> color sel medium orchid
> select /BI
1499 atoms, 1522 bonds, 1 pseudobond, 186 residues, 2 models selected
> color sel brown
> select /BR
295 atoms, 297 bonds, 39 residues, 1 model selected
> color sel spring green
> select /BV
633 atoms, 642 bonds, 81 residues, 1 model selected
> color sel saddle brown
> select /BW
1034 atoms, 1052 bonds, 129 residues, 1 model selected
> color sel orange red
> select /BX
1077 atoms, 1096 bonds, 139 residues, 1 model selected
> color sel dark salmon
[Repeated 1 time(s)]
> color sel salmon
> color sel dark salmon
> select /BY
1007 atoms, 1021 bonds, 124 residues, 1 model selected
> select /Ad
25071 atoms, 28044 bonds, 13 pseudobonds, 1173 residues, 2 models selected
> color sel dodger blue
> select /BY
1007 atoms, 1021 bonds, 124 residues, 1 model selected
> color sel dark gray
> select /BW
1034 atoms, 1052 bonds, 129 residues, 1 model selected
> select /BX
1077 atoms, 1096 bonds, 139 residues, 1 model selected
> select /BY
1007 atoms, 1021 bonds, 124 residues, 1 model selected
> color sel old lace
> select /Ad:418
21 atoms, 22 bonds, 1 residue, 1 model selected
> select up
25071 atoms, 28044 bonds, 1173 residues, 1 model selected
> select up
47873 atoms, 51194 bonds, 4085 residues, 1 model selected
> select down
25071 atoms, 28044 bonds, 1173 residues, 1 model selected
> color sel powder blue
> select clear
> select /Ad
25071 atoms, 28044 bonds, 13 pseudobonds, 1173 residues, 2 models selected
> color sel dodger blue
> select clear
> select /Ba
786 atoms, 801 bonds, 97 residues, 1 model selected
> color sel powder blue
> select /Bb
654 atoms, 665 bonds, 85 residues, 1 model selected
> color sel dark slate gray
> select /Be
353 atoms, 357 bonds, 1 pseudobond, 44 residues, 2 models selected
> color sel dark cyan
> color sel sandy brown
> select /Cn
238 atoms, 239 bonds, 25 residues, 1 model selected
> color sel light pink
> color sel black
> color sel violet
> select clear
> set bgColor white
> set bgColor #eeeeec
> set bgColor #d3d7cf
> set bgColor black
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> select /Cn:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
203 atoms, 204 bonds, 21 residues, 1 model selected
> select up
238 atoms, 239 bonds, 25 residues, 1 model selected
> select up
47873 atoms, 51194 bonds, 4085 residues, 1 model selected
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure.pdb
> selectedOnly true relModel #3
> hide #!3 models
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure.pdb
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure.pdb
---
warning | Cannot find LINK/SSBOND residue G (423 )
Chain information for 40S_body_figure.pdb #1
---
Chain | Description
Ad | No description available
BA | No description available
BB | No description available
BC | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BL | No description available
BN | No description available
BO | No description available
BR | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
Ba | No description available
Bb | No description available
Be | No description available
Cn | No description available
> show #!1 cartoons
> hide #!1 atoms
> close #1
> show #!3 models
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure.pdb
> selectedOnly true relModel #3
> hide #!3 models
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure.pdb
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure.pdb
---
warning | Cannot find LINK/SSBOND residue G (423 )
Chain information for 40S_body_figure.pdb #1
---
Chain | Description
Ad | No description available
BA | No description available
BB | No description available
BC | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BL | No description available
BN | No description available
BO | No description available
BR | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
Ba | No description available
Bb | No description available
Be | No description available
Cn | No description available
> show #!1 cartoons
> hide #!1 atoms
> close #1
> show #!3 models
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_fig.cif
> selectedOnly true relModel #3
Not saving entity_poly_seq for non-authoritative sequences
> hide #!3 models
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_fig.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_fig.cif
---
warnings | Unknown polymer entity '1' near line 201
Unknown polymer entity '2' near line 25272
Unknown polymer entity '3' near line 26826
Unknown polymer entity '4' near line 28554
Unknown polymer entity '5' near line 30261
16 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 40S_body_fig.cif #1
---
Chain | Description
Ad | ?
BA | ?
BB | ?
BC | ?
BE | ?
BG | ?
BH | ?
BI | ?
BJ | ?
BL | ?
BN | ?
BO | ?
BR | ?
BV | ?
BW | ?
BX | ?
BY | ?
Ba | ?
Bb | ?
Be | ?
Cn | ?
> show #!1 cartoons
> hide #!1 atoms
> close #1
> open /home/user3/Documents/ribosome_references_80S/80S_without_head/7qix.pdb
7qix.pdb title:
Specific features and methylation sites of A plant ribosome. 40S body
ribosomal subunit. [more info...]
Chain information for 7qix.pdb #1
---
Chain | Description | UniProt
2 | 18S RRNA body |
D | 60S ribosomal protein L41 | K4C3A4_SOLLC
E | 40S ribosomal protein sa |
F | 40S ribosomal protein S3A |
G | 40S body ribosomal protein ES4 |
H | 40S ribosomal protein S7 |
I | 40S ribosomal protein S8 |
J | ribosomal_S17_N domain-containing protein | K4C998_SOLLC
K | 40S ribosomal protein S17 | RS17_SOLLC
L | 40S ribosomal protein S21 |
M | 40S body ribosomal protein US12 | K4D3L7_SOLLC
N | 40S ribosomal protein S26 |
O | S5 DRBM domain-containing protein |
P | 40S ribosomal protein S6 |
Q | 40S body ribosomal protein US4 | K4ATQ2_SOLLC
R | 30S ribosomal protein S15, chloroplastic | K4CYU9_SOLLC
S | ribosomal protein S14-LIKE | Q38JI8_SOLTU
T | 40S ribosomal protein S15A-1 isoform X1 |
U | 40S ribosomal protein S24 |
V | 40S ribosomal protein S27 |
W | 40S ribosomal protein S30 |
X | ribosomal protein L19 |
Non-standard residues in 7qix.pdb #1
---
IAS — β-L-aspartic acid (L-aspartic acid)
K — potassium ion
MG — magnesium ion
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
> show #!3 models
> select #1
84097 atoms, 86664 bonds, 384 pseudobonds, 4672 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_fig.cif
> models #3 selectedOnly true relModel #3
Not saving entity_poly_seq for non-authoritative sequences
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_fig.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_fig.cif
---
warnings | Unknown polymer entity '1' near line 201
Unknown polymer entity '2' near line 25272
Unknown polymer entity '3' near line 26826
Unknown polymer entity '4' near line 28554
Unknown polymer entity '5' near line 30261
16 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 40S_body_fig.cif #2
---
Chain | Description
Ad | ?
BA | ?
BB | ?
BC | ?
BE | ?
BG | ?
BH | ?
BI | ?
BJ | ?
BL | ?
BN | ?
BO | ?
BR | ?
BV | ?
BW | ?
BX | ?
BY | ?
Ba | ?
Bb | ?
Be | ?
Cn | ?
> hide #!1 models
> hide #!3 models
> show #!2 cartoons
> hide #!2 atoms
> show #!3 models
> hide #!2 models
> close #2
> close #1
> select clear
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure_colored.cxs
——— End of log from Sat Aug 20 22:03:35 2022 ———
opened ChimeraX session
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure_colored
'/home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure_colored'
has no suffix
> open
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure_colored.cx
Unrecognized file suffix '.cx'
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> save
> /home/user3/Documents/ribosome_references_80S/80S_without_head/40S_body_figure_colored1.cxs
> select clear
> open /home/user3/Documents/ribosome_references_80S/Douse_20/douse_000.pdb
Chain information for douse_000.pdb #1
---
Chain | Description
Ad | No description available
BA | No description available
BB | No description available
BC | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BL | No description available
BN | No description available
BO | No description available
BR | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
Ba | No description available
Bb | No description available
Be | No description available
Cn | No description available
> hide #!3 models
> open
> /home/user3/Documents/ribosome_references_80S/40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc
Opened 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 1.07, shown at level 0.591, step 2, values float32
> ui tool show "Hide Dust"
> surface dust #2 size 35
> show #!1 cartoons
> hide #!1 atoms
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> show #!3 models
> hide #!3 models
> ~select #3
Nothing selected
> select #1
48512 atoms, 51193 bonds, 15 pseudobonds, 4724 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-8.1798,0,1,0,-18.469,0,0,1,-5.0001
> view matrix models
> #1,-0.31934,-0.3764,-0.86968,629.71,-0.84795,0.52324,0.084902,257.55,0.42309,0.76455,-0.48626,157.68
> view matrix models
> #1,-0.69227,-0.50524,0.51526,336.06,-0.70955,0.60672,-0.35838,337.36,-0.13155,-0.6137,-0.77851,691.34
> view matrix models
> #1,0.013665,0.85592,0.51693,-141.87,-0.99127,0.079384,-0.10524,449.77,-0.13111,-0.51098,0.84953,188.64
> view matrix models
> #1,-0.66184,-0.37128,0.65124,257.8,-0.66915,0.68423,-0.28995,290.02,-0.33795,-0.62768,-0.70129,717.89
> view matrix models
> #1,-0.66184,-0.37128,0.65124,271.12,-0.66915,0.68423,-0.28995,329.24,-0.33795,-0.62768,-0.70129,583.73
> view matrix models
> #1,-0.81625,-0.44431,0.36923,405.56,-0.54546,0.80328,-0.2392,258.77,-0.19032,-0.39664,-0.89803,554.31
> view matrix models
> #1,-0.89399,-0.43989,0.08538,505.24,-0.44795,0.88223,-0.14496,190.79,-0.011557,-0.16784,-0.98575,486.46
> view matrix models
> #1,-0.84617,-0.49366,0.20074,473.35,-0.52684,0.83162,-0.17564,229.28,-0.080232,-0.25438,-0.96377,515.65
> view matrix models
> #1,-0.83781,-0.52768,0.14012,497.3,-0.5449,0.8242,-0.15419,228.74,-0.034128,-0.20553,-0.97805,498.09
> view matrix models
> #1,-0.83781,-0.52768,0.14012,488.63,-0.5449,0.8242,-0.15419,211.17,-0.034128,-0.20553,-0.97805,496.34
> view matrix models
> #1,-0.82161,-0.56773,-0.051382,550.72,-0.56497,0.82298,-0.05929,188.03,0.075947,-0.019684,-0.99692,433.65
> view matrix models
> #1,-0.92157,-0.38576,0.043449,502.3,-0.38265,0.92155,0.065851,87.474,-0.065443,0.044061,-0.99688,450.12
> ui tool show "Fit in Map"
Fit molecule douse_000.pdb (#1) to map
40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) using 48512 atoms
average map value = 1.799, steps = 188
shifted from previous position = 5.14
rotated from previous position = 19.2 degrees
atoms outside contour = 5213, contour level = 0.59137
Position of douse_000.pdb (#1) relative to
40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.99789897 -0.06278185 0.01600343 458.66717435
-0.06201671 0.99708231 0.04450637 4.90769397
-0.01875093 0.04342038 -0.99888092 442.80716772
Axis -0.03122484 0.99927025 0.02199943
Axis point 231.33687483 0.00000000 219.35386903
Rotation angle (degrees) 179.00358340
Shift along axis 0.32381132
> save /home/user3/Documents/ribosome_references_80S/douse_40S_body.cif models
> #1 selectedOnly true relModel #2
Not saving entity_poly_seq for non-authoritative sequences
> hide #!1 models
> ~select #1
Nothing selected
> open /home/user3/Documents/ribosome_references_80S/douse_40S_body.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/douse_40S_body.cif
---
warnings | Unknown polymer entity '1' near line 243
Unknown polymer entity '2' near line 25314
Unknown polymer entity '3' near line 26868
Unknown polymer entity '4' near line 28596
Unknown polymer entity '5' near line 30303
16 messages similar to the above omitted
Unable to fetch template for 'HOHA': might have incorrect bonds
Unable to fetch template for 'HOHB': might have incorrect bonds
Unable to fetch template for 'HOHC': might have incorrect bonds
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for douse_40S_body.cif #4
---
Chain | Description
Ad | ?
BA | ?
BB | ?
BC | ?
BE | ?
BG | ?
BH | ?
BI | ?
BJ | ?
BL | ?
BN | ?
BO | ?
BR | ?
BV | ?
BW | ?
BX | ?
BY | ?
Ba | ?
Bb | ?
Be | ?
Cn | ?
> close #2
> show #!1 models
> close #1
> show #!3 models
> select #4
48512 atoms, 51193 bonds, 15 pseudobonds, 4724 residues, 2 models selected
> close #4
> open /home/user3/Documents/ribosome_references_80S/douse_40S_body.cif
Summary of feedback from opening
/home/user3/Documents/ribosome_references_80S/douse_40S_body.cif
---
warnings | Unknown polymer entity '1' near line 243
Unknown polymer entity '2' near line 25314
Unknown polymer entity '3' near line 26868
Unknown polymer entity '4' near line 28596
Unknown polymer entity '5' near line 30303
16 messages similar to the above omitted
Unable to fetch template for 'HOHA': might have incorrect bonds
Unable to fetch template for 'HOHB': might have incorrect bonds
Unable to fetch template for 'HOHC': might have incorrect bonds
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for douse_40S_body.cif #1
---
Chain | Description
Ad | ?
BA | ?
BB | ?
BC | ?
BE | ?
BG | ?
BH | ?
BI | ?
BJ | ?
BL | ?
BN | ?
BO | ?
BR | ?
BV | ?
BW | ?
BX | ?
BY | ?
Ba | ?
Bb | ?
Be | ?
Cn | ?
> open
> /home/user3/Documents/ribosome_references_80S/40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc
Opened 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 1.07, shown at level 0.591, step 2, values float32
> select #1
48512 atoms, 51193 bonds, 15 pseudobonds, 4724 residues, 2 models selected
> save /home/user3/Documents/ribosome_references_80S/douse_40S_body.pdb models
> #1 selectedOnly true relModel #2
> close #1
> open /home/user3/Documents/ribosome_references_80S/douse_40S_body.pdb
Chain information for douse_40S_body.pdb #1
---
Chain | Description
Ad | No description available
BA | No description available
BB | No description available
BC | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BL | No description available
BN | No description available
BO | No description available
BR | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
Ba | No description available
Bb | No description available
Be | No description available
Cn | No description available
> close #1
> ui tool show "Hide Dust"
> surface dust #2 size 30
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> view matrix models
> #3,0.39075,-0.25655,0.88402,76.081,-0.59034,0.66703,0.45451,-85.326,-0.70627,-0.69947,0.10919,383.2
> view matrix models
> #3,-0.70989,-0.6112,0.34998,561.52,-0.17704,0.63581,0.75127,-257.21,-0.6817,0.47136,-0.55956,298.77
> view matrix models
> #3,0.2292,-0.36125,0.90386,130.85,0.28353,0.91309,0.29304,-290.34,-0.93117,0.18911,0.3117,164.68
> view matrix models
> #3,-0.76598,0.24395,-0.59478,650.44,-0.34946,0.61856,0.70375,-200.8,0.53959,0.74691,-0.38856,-88.233
> view matrix models
> #3,-0.59934,-0.70549,-0.37826,773.1,-0.54494,0.70571,-0.45278,162.09,0.58637,-0.065241,-0.80741,215.53
> view matrix models
> #3,-0.97489,-0.11688,0.18955,551.36,-0.19706,0.84924,-0.48986,61.766,-0.10372,-0.51492,-0.85094,487.77
> view matrix models
> #3,-0.39673,0.60097,0.69385,105.53,-0.69033,0.30288,-0.65705,349.27,-0.60502,-0.73966,0.29471,315.59
> view matrix models
> #3,0.019491,0.90262,0.42999,19.431,-0.94377,0.15857,-0.29008,331.82,-0.33002,-0.40016,0.85496,9.8392
> view matrix models
> #3,0.1764,0.98185,-0.069742,112.71,-0.9832,0.17913,0.035033,240.21,0.04689,0.06239,0.99695,-224.64
> view matrix models
> #3,-0.84196,-0.31506,-0.43799,752.81,-0.37192,0.92702,0.048126,-75.703,0.39086,0.20342,-0.89769,222.38
> view matrix models
> #3,-0.94447,-0.32395,-0.055048,665.19,-0.31494,0.94022,-0.12959,-39.27,0.093739,-0.10506,-0.99004,388.25
> view matrix models
> #3,-0.69905,-0.17303,0.69382,354.97,-0.586,0.69466,-0.41719,163.38,-0.40979,-0.69822,-0.587,521.48
> view matrix models
> #3,-0.58336,-0.52697,0.61805,434.75,-0.7947,0.52752,-0.30031,214.82,-0.16778,-0.66635,-0.72651,501.1
> view matrix models
> #3,-0.58336,-0.52697,0.61805,382.85,-0.7947,0.52752,-0.30031,344.91,-0.16778,-0.66635,-0.72651,634.51
> view matrix models
> #3,-0.58336,-0.52697,0.61805,419.89,-0.7947,0.52752,-0.30031,344.61,-0.16778,-0.66635,-0.72651,591.73
> view matrix models
> #3,-0.58336,-0.52697,0.61805,362.47,-0.7947,0.52752,-0.30031,375.11,-0.16778,-0.66635,-0.72651,675.06
> view matrix models
> #3,-0.58336,-0.52697,0.61805,304.4,-0.7947,0.52752,-0.30031,386.09,-0.16778,-0.66635,-0.72651,748.08
> view matrix models
> #3,-0.61131,-0.73915,0.28276,459.07,-0.78884,0.59778,-0.14278,321.96,-0.063496,-0.31034,-0.9485,706.34
> view matrix models
> #3,-0.51769,-0.44207,0.73251,236.16,-0.82821,0.47373,-0.29942,405.94,-0.21465,-0.76167,-0.61137,747.11
> view matrix models
> #3,-0.61342,-0.69545,0.37426,422.37,-0.77459,0.62222,-0.11337,304.39,-0.15403,-0.35944,-0.92037,729.78
> view matrix models
> #3,-0.61263,-0.64889,0.45125,388.62,-0.76788,0.62387,-0.14538,311.92,-0.18719,-0.43557,-0.88047,743.35
> view matrix models
> #3,-0.38155,-0.92252,-0.058026,551.21,-0.92326,0.3834,-0.024443,367.55,0.044797,0.044246,-0.99802,613.35
> view matrix models
> #3,-0.3719,-0.12757,0.91947,74.761,-0.7312,0.65048,-0.2055,315.16,-0.57188,-0.74874,-0.33519,742.44
> view matrix models
> #3,-0.83387,-0.36832,0.4111,383.66,-0.35955,0.92756,0.10173,76.929,-0.41879,-0.062983,-0.9059,714.72
> view matrix models
> #3,-0.56698,-0.8234,-0.023183,558.94,-0.82142,0.56728,-0.058841,311.72,0.061601,-0.014319,-0.998,623.38
> view matrix models
> #3,-0.75246,-0.45587,-0.47537,646.65,-0.19796,0.84492,-0.49691,236.32,0.62818,-0.2798,-0.72602,479.77
> view matrix models
> #3,-0.88677,0.1994,-0.41699,505.21,0.45394,0.54562,-0.70444,222.58,0.087046,-0.81397,-0.57435,681.36
> view matrix models
> #3,-0.95078,-0.1965,0.23959,419.67,-0.21813,0.97361,-0.067113,84.225,-0.22007,-0.11607,-0.96855,701.38
> view matrix models
> #3,-0.88502,-0.13297,0.44615,329.37,-0.22426,0.96159,-0.15826,115.2,-0.40797,-0.24012,-0.88085,746.63
> view matrix models
> #3,-0.79479,-0.60245,0.073159,529.36,-0.60541,0.77872,-0.16452,244.93,0.042144,-0.17505,-0.98366,661.31
> view matrix models
> #3,-0.81621,-0.49831,0.29238,445.2,-0.56726,0.78722,-0.24189,257.18,-0.10963,-0.36329,-0.92521,722.22
> view matrix models
> #3,-0.81621,-0.49831,0.29238,439.54,-0.56726,0.78722,-0.24189,257.78,-0.10963,-0.36329,-0.92521,729.07
> view matrix models
> #3,-0.62268,-0.064398,0.77982,151.11,-0.61318,0.65926,-0.43518,354.91,-0.48608,-0.74915,-0.45,764.03
> view matrix models
> #3,-0.75222,-0.65646,0.056762,531.74,-0.65342,0.75428,0.06412,194.78,-0.084907,0.011143,-0.99633,656.37
> view matrix models
> #3,-0.89526,-0.42287,-0.14031,566.55,-0.37818,0.88773,-0.26251,198.09,0.23556,-0.18195,-0.95467,618.21
> view matrix models
> #3,-0.84898,-0.48968,0.19863,472.35,-0.51167,0.66784,-0.54054,361.26,0.13204,-0.56054,-0.81753,690.04
> view matrix models
> #3,-0.8714,-0.36329,0.32967,409.1,-0.45955,0.83969,-0.28939,235.41,-0.17168,-0.40367,-0.89865,744.59
> view matrix models
> #3,-0.8714,-0.36329,0.32967,494.44,-0.45955,0.83969,-0.28939,200.3,-0.17168,-0.40367,-0.89865,626.53
> ~select #3
Nothing selected
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> view matrix models
> #3,-0.8714,-0.36329,0.32967,394.16,-0.45955,0.83969,-0.28939,244.61,-0.17168,-0.40367,-0.89865,565.11
> view matrix models
> #3,-0.8714,-0.36329,0.32967,411.09,-0.45955,0.83969,-0.28939,237.16,-0.17168,-0.40367,-0.89865,552.25
> view matrix models
> #3,-0.8714,-0.36329,0.32967,410.23,-0.45955,0.83969,-0.28939,232.39,-0.17168,-0.40367,-0.89865,557.41
> view matrix models
> #3,-0.9402,-0.32017,0.11626,478.11,-0.33127,0.9389,-0.093392,122.89,-0.079255,-0.12632,-0.98882,498.07
> view matrix models
> #3,-0.9402,-0.32017,0.11626,479.35,-0.33127,0.9389,-0.093392,125.55,-0.079255,-0.12632,-0.98882,495.6
Fit molecule 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3) to
map 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) using 47873 atoms
average map value = 1.81, steps = 176
shifted from previous position = 8.39
rotated from previous position = 18.5 degrees
atoms outside contour = 4991, contour level = 0.59137
Position of 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3)
relative to 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99790560 -0.06265703 0.01607833 458.63138139
-0.06188836 0.99708938 0.04452659 4.88429780
-0.01882143 0.04343827 -0.99887882 442.81387713
Axis -0.03116146 0.99927202 0.02200882
Axis point 231.32654051 0.00000000 219.34927007
Rotation angle (degrees) 178.99941616
Shift along axis 0.33493307
> view matrix models
> #3,-0.99791,-0.062657,0.016078,459.23,-0.061888,0.99709,0.044527,4.4009,-0.018821,0.043438,-0.99888,442.81
Fit molecule 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3) to
map 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) using 47873 atoms
average map value = 1.81, steps = 68
shifted from previous position = 0.769
rotated from previous position = 0.000327 degrees
atoms outside contour = 4993, contour level = 0.59137
Position of 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3)
relative to 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99790565 -0.06265671 0.01607675 458.63461252
-0.06188801 0.99708916 0.04453206 4.88449168
-0.01882019 0.04344383 -0.99887860 442.81327884
Axis -0.03116129 0.99927197 0.02201158
Axis point 231.32799944 0.00000000 219.34910985
Rotation angle (degrees) 178.99949715
Shift along axis 0.33631065
> ~select #3
Nothing selected
> select #2
2 models selected
> ~select #2
Nothing selected
> select #2
2 models selected
> ui tool show "Color Actions"
> color zone #2 near #3 distance 6.42
> ~select #2
Nothing selected
> hide #!3 models
> volume #2 step 1
> volume #2 level 0.7
> volume #2 step 2
> volume #2 level 0.5
> volume #2 level 0.4
> volume #2 level 0.45
> volume #2 level 0.48
> vop gaussian #2 sdev 3.21
Opened 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc gaussian as #1,
grid size 420,420,420, pixel 1.07, shown at step 1, values float32
> show #!2 models
> hide #!1 models
> close #1
> volume #2 level 0.75
> volume #2 step 1
> volume #2 level 0.8
> volume #2 level 0.85
> set bgColor white
> volume #2 step 2
> volume #2 level 0.45
> volume #2 level 0.5
> volume #2 level 0.55
> volume #2 step 1
> volume #2 level 0.75
> volume #2 level 0.7
> volume #2 level 0.78
> volume #2 level 0.75
> volume #2 level 0.76
> volume #2 level 0.78
> turn 180
Expected an axis vector or a keyword
> turn y 360 models #2 center #2
> turn y 1 360 models #2 center #2
> turn y 1 180 models #2 center #2
[Repeated 5 time(s)]
> save /home/user3/Desktop/image9.png supersample 3
> turn y 1 180 models #2 center #2
> save /home/user3/Desktop/image10.png supersample 3
> show #!3 models
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> view matrix models
> #3,-0.99791,-0.062657,0.016077,441.14,-0.061888,0.99709,0.044532,15.683,-0.01882,0.043444,-0.99888,472.03
> view matrix models
> #3,-0.90186,0.34096,-0.26532,408.13,0.16889,0.84349,0.5099,-137.76,0.39765,0.41505,-0.8183,235.87
> view matrix models
> #3,-0.46689,0.8395,-0.27795,197.7,-0.79811,-0.26466,0.54127,329.06,0.38083,0.47455,0.79358,-248.07
> view matrix models
> #3,-0.67314,0.73939,0.013997,181.38,-0.73943,-0.67323,0.0026391,570.41,0.011375,-0.0085735,0.9999,-112.77
> view matrix models
> #3,-0.95359,0.086562,-0.28839,486.29,-0.21326,-0.87031,0.44394,369.94,-0.21256,0.48484,0.84838,-134.48
> view matrix models
> #3,-0.71983,0.61347,-0.32479,320.96,-0.68706,-0.56299,0.45933,398.6,0.098935,0.55379,0.82676,-213.7
> view matrix models
> #3,-0.58678,0.80083,-0.11983,187.02,-0.80277,-0.5947,-0.043415,579.57,-0.10603,0.070718,0.99185,-102.92
> view matrix models
> #3,-0.85453,0.34846,-0.38517,431.05,-0.42223,-0.89791,0.1244,516.87,-0.3025,0.26894,0.91442,-83.06
> view matrix models
> #3,-0.3007,0.91249,-0.27739,143.36,-0.91781,-0.19781,0.34423,397.89,0.25923,0.3581,0.89698,-223.98
> view matrix models
> #3,-0.40244,0.89384,-0.19769,146.98,-0.91142,-0.41145,-0.0049477,549.34,-0.085761,0.17818,0.98025,-129.31
> view matrix models
> #3,-0.40244,0.89384,-0.19769,165.4,-0.91142,-0.41145,-0.0049477,540.29,-0.085761,0.17818,0.98025,-155.97
> ui tool show "Fit in Map"
Fit molecule 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3) to
map 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) using 47873 atoms
average map value = 1.81, steps = 172
shifted from previous position = 4.5
rotated from previous position = 16.9 degrees
atoms outside contour = 6312, contour level = 0.78
Position of 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3)
relative to 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99789659 -0.06282252 0.01599247 458.68538052
-0.06205780 0.99707968 0.04450818 4.92234011
-0.01874189 0.04342210 -0.99888102 442.80167966
Axis -0.03124530 0.99926960 0.02200007
Axis point 231.34512596 0.00000000 219.35202892
Rotation angle (degrees) 179.00415650
Shift along axis 0.32864877
> ~select #3
Nothing selected
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> select #2
2 models selected
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> save /home/user3/Documents/ribosome_references_80S/40S_body_figure_final.cxs
> includeMaps true
——— End of log from Tue Aug 23 01:09:00 2022 ———
opened ChimeraX session
> open
> /home/user3/Documents/Composite_map_40S_wheat_AUG2022/3JAM_aligned_head_trial_zflipped_resampled4201.mrc
Opened 3JAM_aligned_head_trial_zflipped_resampled4201.mrc as #1, grid size
420,420,420, pixel 1.07, shown at level 0.000174, step 2, values float32
> open /home/user3/Documents/Composite_map_40S_wheat_AUG2022/375_zflipped.mrc
Opened 375_zflipped.mrc as #4, grid size 420,420,420, pixel 1.07, shown at
level 1.33, step 2, values float32
> volume #4 level 0.7
> select #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-1.0889,0,1,0,1.7392,0,0,1,0.18492
> ui tool show "Fit in Map"
Fit map 3JAM_aligned_head_trial_zflipped_resampled4201.mrc in map
375_zflipped.mrc using 57734 points
correlation = 0.903, correlation about mean = 0.6152, overlap = 2.91e+04
steps = 88, shift = 2.02, angle = 0.106 degrees
Position of 3JAM_aligned_head_trial_zflipped_resampled4201.mrc (#1) relative
to 375_zflipped.mrc (#4) coordinates:
Matrix rotation and translation
0.99999830 -0.00171715 0.00067164 0.34824778
0.00171711 0.99999852 0.00006891 -0.47018091
-0.00067176 -0.00006775 0.99999977 0.22026026
Axis -0.03703372 0.36404586 0.93064446
Axis point 278.43158822 202.98109376 0.00000000
Rotation angle (degrees) 0.10571626
Shift along axis 0.02091967
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> view matrix models
> #3,-0.16093,0.96733,-0.19587,95.303,-0.95844,-0.20054,-0.20292,556.85,-0.23557,0.15508,0.95941,-114.62
> select #2
2 models selected
> view matrix models
> #2,0.096687,0.96578,0.24067,-116.4,0.96578,-0.1495,0.21194,18.867,0.24067,0.21194,-0.94718,250.16
> view matrix models
> #2,0.096687,0.96578,0.24067,-175.95,0.96578,-0.1495,0.21194,93.619,0.24067,0.21194,-0.94718,345.81
> view matrix models
> #2,0.096687,0.96578,0.24067,-170.13,0.96578,-0.1495,0.21194,96.047,0.24067,0.21194,-0.94718,340.94
> view matrix models
> #2,0.6088,-0.30025,0.73431,-59.056,0.64804,0.72214,-0.242,29.431,-0.45762,0.62319,0.63421,154.35
> view matrix models
> #2,0.98521,-0.13383,-0.10696,-53.838,0.022684,0.72072,-0.69285,243.31,0.16981,0.68018,0.7131,-15.276
> view matrix models
> #2,0.59564,-0.49917,-0.62932,205.06,0.35831,0.86631,-0.34801,77.506,0.71891,-0.018205,0.69487,30.414
> view matrix models
> #2,-0.086935,-0.93732,-0.33745,421.29,0.97547,-0.011328,-0.21984,127.98,0.20224,-0.34828,0.91531,193.79
> view matrix models
> #2,-0.85226,-0.3899,0.34875,357.1,-0.36672,-0.030127,-0.92985,550.55,0.37306,-0.92036,-0.11731,454.09
> view matrix models
> #2,-0.89201,0.28673,0.34944,202.87,-0.44657,-0.43928,-0.77949,644.02,-0.069999,-0.85136,0.51989,439.22
> view matrix models
> #2,-0.22494,0.81312,-0.53687,61.795,-0.90899,-0.37355,-0.18492,641.04,-0.35092,0.44642,0.82315,143.05
> view matrix models
> #2,-0.11642,0.18459,-0.9759,257.2,-0.90903,-0.41567,0.029821,617.64,-0.40014,0.89059,0.21619,142.03
> view matrix models
> #2,-0.23364,-0.34944,-0.90736,402.12,-0.66924,-0.61917,0.41078,552.33,-0.70536,0.70322,-0.089192,304.78
> view matrix models
> #2,-0.46709,-0.49767,-0.73086,463.7,-0.25574,-0.7152,0.65045,443.44,-0.84642,0.49073,0.20679,342.05
> view matrix models
> #2,-0.44837,-0.021862,-0.89358,370.08,-0.68535,-0.63336,0.35939,567.47,-0.57381,0.77355,0.269,201.74
> view matrix models
> #2,-0.44837,-0.021862,-0.89358,467.86,-0.68535,-0.63336,0.35939,463.69,-0.57381,0.77355,0.269,53.399
> view matrix models
> #2,-0.44837,-0.021862,-0.89358,479.21,-0.68535,-0.63336,0.35939,458.41,-0.57381,0.77355,0.269,39.283
> view matrix models
> #2,-0.42413,-0.014428,-0.90549,473.73,-0.68112,-0.65387,0.32945,467.07,-0.59682,0.75647,0.2675,48.901
> view matrix models
> #2,-0.44884,-0.021998,-0.89334,479.32,-0.68542,-0.63296,0.35996,458.24,-0.57336,0.77388,0.26902,39.099
> view matrix models
> #2,-0.98438,0.11185,0.13595,408.69,-0.14955,-0.93874,-0.31048,514.19,0.092895,-0.32596,0.94081,46.979
> view matrix models
> #2,-0.96815,0.1688,-0.18489,441.38,-0.14981,-0.98231,-0.11234,493.79,-0.20058,-0.081065,0.97632,49.498
> view matrix models
> #2,-0.96815,0.1688,-0.18489,439.93,-0.14981,-0.98231,-0.11234,497.14,-0.20058,-0.081065,0.97632,53.734
> view matrix models
> #2,-0.98784,0.14577,-0.05406,428.48,-0.13171,-0.9694,-0.20718,504.76,-0.082606,-0.19754,0.97681,56.078
Fit map 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc in map
375_zflipped.mrc using 434808 points
correlation = 0.9226, correlation about mean = 0.5958, overlap = 7.894e+05
steps = 348, shift = 15.6, angle = 18.1 degrees
Position of 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) relative
to 375_zflipped.mrc (#4) coordinates:
Matrix rotation and translation
-0.99134959 -0.13106304 -0.00695455 477.64734944
0.13124666 -0.98976891 -0.05596199 431.47447227
0.00045115 -0.05639066 0.99840864 11.25195103
Axis -0.00163357 -0.02822138 0.99960036
Axis point 224.61418463 231.63799238 0.00000000
Rotation angle (degrees) 172.46063776
Shift along axis -1.70961984
> close #4
> select #3
47873 atoms, 51194 bonds, 15 pseudobonds, 4085 residues, 2 models selected
> view matrix models
> #3,-0.16093,0.96733,-0.19587,26.979,-0.95844,-0.20054,-0.20292,597.29,-0.23557,0.15508,0.95941,-35.428
> view matrix models
> #3,-0.22658,0.62015,-0.75105,286.44,-0.84986,0.25083,0.4635,271.07,0.47582,0.7433,0.47021,-188.46
> view matrix models
> #3,-0.97125,-0.23793,0.0081066,431.03,-0.23094,0.93337,-0.27475,189.63,0.057804,-0.26872,-0.96148,563.46
> view matrix models
> #3,-0.7824,0.49273,-0.38087,331.38,-0.40235,0.06686,0.91304,82.615,0.47535,0.86761,0.14594,-122.31
> view matrix models
> #3,-0.7281,-0.67632,0.11163,449.62,0.6745,-0.67786,0.29251,200.43,-0.12216,0.28827,0.94972,-89.171
> view matrix models
> #3,0.055985,-0.93637,0.34653,267.2,0.11855,-0.33838,-0.93351,604.64,0.99137,0.093342,0.092058,-39.19
> view matrix models
> #3,0.96044,-0.26593,0.082678,-14.382,-0.21643,-0.89959,-0.37935,648.41,0.17526,0.34645,-0.92155,380.84
> view matrix models
> #3,0.91999,-0.2363,0.3127,-79.945,0.20806,-0.38171,-0.90056,585.22,0.33216,0.89356,-0.30201,35.106
> view matrix models
> #3,0.91999,-0.2363,0.3127,-14.727,0.20806,-0.38171,-0.90056,541.75,0.33216,0.89356,-0.30201,-44.398
> view matrix models
> #3,0.99731,-0.071086,-0.01777,26.301,-0.072862,-0.98778,-0.1378,522.74,-0.0077572,0.13873,-0.9903,411.16
> view matrix models
> #3,0.92713,-0.37473,0.00085022,107.9,-0.37473,-0.92713,-0.0027127,535.98,0.0018048,0.0021964,-1,444
Fit molecule 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3) to
map 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2) using 47873 atoms
average map value = 1.811, steps = 176
shifted from previous position = 18.4
rotated from previous position = 18.1 degrees
atoms outside contour = 6308, contour level = 0.78
Position of 40S_1_after_real_space_refined_real_space_refined_018.pdb (#3)
relative to 40S_body_cryosparc_P2_J323_006_volume_map_sharp.mrc (#2)
coordinates:
Matrix rotation and translation
-0.99789833 -0.06279060 0.01601276 458.67364903
-0.06202493 0.99708154 0.04451370 4.91379553
-0.01876107 0.04342695 -0.99888050 442.80494264
Axis -0.03122901 0.99927005 0.02200244
Axis point 231.34128707 0.00000000 219.35153482
Rotation angle (degrees) 179.00302533
Shift along axis 0.32907209
> open
> /home/user3/Documents/ribosome_references_80S/head_chimera_wrt_map_real_space_refined_011.pdb
Chain information for head_chimera_wrt_map_real_space_refined_011.pdb #4
---
Chain | Description
2 | 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
> show sel cartoons
> hide sel atoms
> select #4
24506 atoms, 25694 bonds, 11 pseudobonds, 2484 residues, 3 models selected
> show sel cartoons
> hide sel atoms
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 2 maps.
[Repeated 1 time(s)]
> hide #!2 models
> hide #!3 models
> color zone #1 near sel & #4 distance 6.42
> show #!3 models
> show #!2 models
> select #4/D
1689 atoms, 1714 bonds, 214 residues, 1 model selected
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> ui tool show "Color Actions"
> color sel maroon
> select #4/E
1476 atoms, 1488 bonds, 1 pseudobond, 195 residues, 2 models selected
> color sel dark orange
> select #4/F
782 atoms, 804 bonds, 92 residues, 1 model selected
> color sel dark khaki
> select #4/G
1019 atoms, 1039 bonds, 127 residues, 1 model selected
> color sel green
> select #4/H
1139 atoms, 1154 bonds, 144 residues, 1 model selected
> color sel purple
> color sel burly wood
> color sel purple
> select #4/I
682 atoms, 689 bonds, 82 residues, 1 model selected
> color sel burly wood
> select #4/J
1162 atoms, 1171 bonds, 150 residues, 1 model selected
> color sel rosy brown
> select #4/K
1129 atoms, 1128 bonds, 165 residues, 1 model selected
> color sel magenta
> select #4/2:1226
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
10050 atoms, 11222 bonds, 472 residues, 1 model selected
> select up
10250 atoms, 11222 bonds, 672 residues, 1 model selected
> color sel dodger blue
> select clear
> select #4/L
828 atoms, 831 bonds, 111 residues, 1 model selected
> color sel forest green
> select #4/M
520 atoms, 522 bonds, 65 residues, 1 model selected
> color sel medium purple
> select #4/N
409 atoms, 416 bonds, 4 pseudobonds, 54 residues, 2 models selected
> color sel lime
> select #4/O
2464 atoms, 2516 bonds, 1 pseudobond, 317 residues, 2 models selected
> color sel yellow
> select #4/P
596 atoms, 598 bonds, 79 residues, 1 model selected
> color sel teal
> select clear
> select #4/Q
299 atoms, 334 bonds, 14 residues, 1 model selected
> show #!1 models
> delete atoms sel
> delete bonds sel
> select #4/R:2
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
62 atoms, 68 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1
2 models selected
> ~select #1
Nothing selected
> select #1
2 models selected
> select #2
2 models selected
> ~select #2
Nothing selected
> select #1
2 models selected
> show #!2 models
> hide #!2 models
> select #4
24145 atoms, 25292 bonds, 11 pseudobonds, 2467 residues, 3 models selected
> ~select #4
Nothing selected
> color zone #1 near #4 distance 6.42
> ui tool show "Color Zone"
> color zone #1 near #4 distance 1.07
> color zone #1 near #4 distance 2
> color zone #1 near #4 distance 20
> color zone #1 near #4 distance 2
> color zone #1 near #4 distance 15
> color zone #1 near #4 distance 16
> color zone #1 near #4 distance 17
> color zone #1 near #4 distance 18
> color zone #1 near #4 distance 19
> color zone #1 near #4 distance 2
> color zone #1 near #4 distance 20
> show #!2 models
> color zone #2 near #4 distance 6.4
> color zone #2 near #4 distance 6
> color zone #2 near #4 distance 2
> color zone #2 near #4 distance 20
> color zone #2 near #4 distance 3
> color zone #2 near #4 distance 30
> color zone #2 near #4 distance 3
> color zone #2 near #4 distance 10
> show #!3 models
> hide #!1 models
> hide #!4 models
> color zone #2 near #3 distance 6.42
> color zone #2 near #4 distance 2
> color zone #2 near #4 distance 20
> color zone #2 near #4 distance 10
> color zone #2 near #4 distance 5
> color zone #2 near #4 distance 50
> color zone #2 near #4 distance 10
> color zone #2 near #4 distance 100
> volume #2 level 0.7
> volume #2 level 0.8
> color zone #2 near #4 distance 10
> color zone #2 near #3 distance 2
> color zone #2 near #3 distance 20
> color zone #2 near #3 distance 22
> color single #2
> color zone #2 near #3 distance 25
> hide #!3 models
> show #!3 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 #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!4 models
> show #!1 models
> volume #1 level 0.0005
> volume #1 level 0.005
> hide #!4 models
> hide #!3 models
> volume #1 level 0.05
> volume #2 level 0.85
> show #!4 models
> show #!3 models
> save /home/user3/Documents/ribosome_references_80S/40S_complete_figure.cxs
> includeMaps true
——— End of log from Thu Sep 1 17:22:15 2022 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Color Actions"
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> select #3/BN
1188 atoms, 1212 bonds, 149 residues, 1 model selected
> select #3/BO
983 atoms, 995 bonds, 130 residues, 1 model selected
> select #3/BR
295 atoms, 297 bonds, 39 residues, 1 model selected
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 249, in _draw_scene
draw_highlight_outline(r, highlight_drawings, color = self._highlight_color,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1569, in draw_highlight_outline
r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1864, in finish_rendering_outline
r.pop_framebuffer()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 714, in pop_framebuffer
fb.activate()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2250, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
OpenGL version: 3.3.0 NVIDIA 470.57.02
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 72 Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz
Cache Size: 25344 KB
Memory:
total used free shared buff/cache available
Mem: 503G 21G 1.9G 87M 480G 480G
Swap: 63G 0B 63G
Graphics:
18:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12ae]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → draw selection: glDrawBuffer: invalid operation |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Graphics worked for a long time, then failed. Not clear why. May be that the graphics context can become invalid on Linux after the machine sleeps and wakes.