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Opened 2 years ago
Last modified 2 years ago
#10338 feedback defect
MemoryError saving session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202307220101 (2023-07-22 01:01:24 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.dev202307220101 (2023-07-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/Session_files/eIF2beta_eIF1A_eIF5placement.cxs"
Log from Mon Aug 28 16:12:33 2023UCSF ChimeraX version: 1.7.dev202307220101
(2023-07-22)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF2beta_intermediates_2.cxs"
Log from Sat May 6 17:06:28 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Jose_TH_43S_PIC\New_RSR_models\open_closed_pdbs.cxs" format session
Log from Wed May 3 14:24:59 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\PhD common folder\OneDrive - Indian Institute of
> Science\Jose_TH_43S_PIC\New_RSR_models\eIF5_displayed_rsr_real_space_refined.cif"
> format mmcif
Summary of feedback from opening D:\PhD common folder\OneDrive - Indian
Institute of
Science\Jose_TH_43S_PIC\New_RSR_models\eIF5_displayed_rsr_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 3872
Missing entity information. Treating each chain as a separate entity.
Missing first residue in struct_conn "C00001"
Missing first residue in struct_conn "C00002"
Missing first residue in struct_conn "C00003"
Missing first residue in struct_conn "C00004"
Missing first residue in struct_conn "C00005"
2838 messages similar to the above omitted
Invalid residue range for struct_conf "17": invalid entity "C", near line 275
Invalid residue range for struct_conf "18": invalid entity "C", near line 276
Invalid residue range for struct_conf "19": invalid entity "C", near line 277
Invalid residue range for struct_conf "20": invalid entity "C", near line 278
Invalid residue range for struct_conf "21": invalid entity "C", near line 279
157 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "F 1": invalid entity "C", near
line 3540
Invalid sheet range for struct_sheet_range "F 2": invalid entity "C", near
line 3541
Invalid sheet range for struct_sheet_range "F 3": invalid entity "C", near
line 3542
Invalid sheet range for struct_sheet_range "F 4": invalid entity "C", near
line 3543
Invalid sheet range for struct_sheet_range "G 1": invalid entity "C", near
line 3544
177 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 91304
Skipping chem_comp category: Missing column 'type' near line 91583
Skipping chem_comp category: Missing column 'type' near line 91844
Skipping chem_comp category: Missing column 'type' near line 92129
Skipping chem_comp category: Missing column 'type' near line 92347
15 messages similar to the above omitted
Chain information for eIF5_displayed_rsr_real_space_refined.cif #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
> set bgColor white
> show cartoons
> hide atoms
> cartoon style width 1 thickness 1
> color #1 #ffaa00ff
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
> show cartoons
> hide atoms
> color #2 cyan
> ui tool show Matchmaker
> matchmaker #!2 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#2), sequence alignment score = 6775.8
RMSD between 1673 pruned atom pairs is 0.858 angstroms; (across all 1780
pairs: 1.400)
> matchmaker #!2 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#2), sequence alignment score = 6775.8
RMSD between 1673 pruned atom pairs is 0.858 angstroms; (across all 1780
pairs: 1.400)
> hide #!2 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/Maps/beta_and_displaced_eif5.mrc"
Opened beta_and_displaced_eif5.mrc as #3, grid size 300,300,300, pixel 1.34,
shown at level 0.0761, step 2, values float32
> volume #3 step 1
> volume #3 level 0.03
> volume #3 level 0.039
> volume #3 level 0.05
> volume #3 level 0.055
> ui tool show "Hide Dust"
> surface dust #3 size 35
> volume #3 level 0.05
> volume #3 level 0.04
> volume #3 level 0.042
> volume #3 level 0.045
> volume #3 style mesh
> show #!2 models
> hide #!2 models
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> show #!2 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/Maps/beta_and_displaced_eif5_gauss134.mrc"
Opened beta_and_displaced_eif5_gauss134.mrc as #4, grid size 300,300,300,
pixel 1.34, shown at level 0.0637, step 2, values float32
> hide #!3 models
> volume #4 step 1
> volume #4 level 0.05902
> volume #4 level 0.05
> volume #4 level 0.03
> volume #4 level 0.035
> surface dust #4 size 35
> volume #4 level 0.03
> volume #4 level 0.02
> volume #4 level 0.01
> volume #4 level 0.015
> volume #4 level 0.018
> volume #4 level 0.02
> volume #4 style mesh
> hide #!2 models
> color #4 #ff557fff models
> color #4 #550000ff models
> color #4 #aa00ffff models
> color #4 #555500ff models
> color #4 #55aa7fff models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> close #3.1
> close #3
> hide #!4 models
> show #!2 models
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 191045 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide atoms
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/beta_no1_cl2_rsr_real_space_refined.cif"
> "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/beta_no1_cl3_rsr_real_space_refined.cif"
Summary of feedback from opening D:/PhD common folder/OneDrive - Indian
Institute of
Science/Jose_TH_43S_PIC/New_RSR_models/beta_no1_cl2_rsr_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 3909
Missing entity information. Treating each chain as a separate entity.
Missing first residue in struct_conn "C00001"
Missing first residue in struct_conn "C00002"
Missing first residue in struct_conn "C00003"
Missing first residue in struct_conn "C00004"
Missing first residue in struct_conn "C00005"
2863 messages similar to the above omitted
Invalid residue range for struct_conf "18": invalid entity "C", near line 274
Invalid residue range for struct_conf "19": invalid entity "C", near line 275
Invalid residue range for struct_conf "20": invalid entity "C", near line 276
Invalid residue range for struct_conf "21": invalid entity "C", near line 277
Invalid residue range for struct_conf "22": invalid entity "C", near line 278
159 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "F 1": invalid entity "C", near
line 3569
Invalid sheet range for struct_sheet_range "F 2": invalid entity "C", near
line 3570
Invalid sheet range for struct_sheet_range "F 3": invalid entity "C", near
line 3571
Invalid sheet range for struct_sheet_range "G 1": invalid entity "C", near
line 3572
Invalid sheet range for struct_sheet_range "G 2": invalid entity "C", near
line 3573
182 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 91161
Skipping chem_comp category: Missing column 'type' near line 91440
Skipping chem_comp category: Missing column 'type' near line 91701
Skipping chem_comp category: Missing column 'type' near line 91986
Skipping chem_comp category: Missing column 'type' near line 92204
15 messages similar to the above omitted
Summary of feedback from opening D:/PhD common folder/OneDrive - Indian
Institute of
Science/Jose_TH_43S_PIC/New_RSR_models/beta_no1_cl3_rsr_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 3909
Missing entity information. Treating each chain as a separate entity.
Missing first residue in struct_conn "C00001"
Missing first residue in struct_conn "C00002"
Missing first residue in struct_conn "C00003"
Missing first residue in struct_conn "C00004"
Missing first residue in struct_conn "C00005"
2857 messages similar to the above omitted
Invalid residue range for struct_conf "17": invalid entity "C", near line 273
Invalid residue range for struct_conf "18": invalid entity "C", near line 274
Invalid residue range for struct_conf "19": invalid entity "C", near line 275
Invalid residue range for struct_conf "20": invalid entity "C", near line 276
Invalid residue range for struct_conf "21": invalid entity "C", near line 277
157 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "F 1": invalid entity "C", near
line 3564
Invalid sheet range for struct_sheet_range "F 2": invalid entity "C", near
line 3565
Invalid sheet range for struct_sheet_range "F 3": invalid entity "C", near
line 3566
Invalid sheet range for struct_sheet_range "G 1": invalid entity "C", near
line 3567
Invalid sheet range for struct_sheet_range "G 2": invalid entity "C", near
line 3568
184 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 91126
Skipping chem_comp category: Missing column 'type' near line 91405
Skipping chem_comp category: Missing column 'type' near line 91666
Skipping chem_comp category: Missing column 'type' near line 91951
Skipping chem_comp category: Missing column 'type' near line 92169
15 messages similar to the above omitted
Chain information for beta_no1_cl2_rsr_real_space_refined.cif #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
Chain information for beta_no1_cl3_rsr_real_space_refined.cif #5
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> show cartoons
> hide atoms
> hide #!3 models
> show #!3 models
> color #3 #55ff00ff
> color #3 yellow
> color #5 #ff5500ff
> color #5 red
> ui tool show Matchmaker
> matchmaker #!3 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
beta_no1_cl2_rsr_real_space_refined.cif, chain 2 (#3), sequence alignment
score = 7196
RMSD between 1736 pruned atom pairs is 0.842 angstroms; (across all 1798
pairs: 0.948)
> matchmaker #!3 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
beta_no1_cl2_rsr_real_space_refined.cif, chain 2 (#3), sequence alignment
score = 7196
RMSD between 1736 pruned atom pairs is 0.842 angstroms; (across all 1798
pairs: 0.948)
> ui tool show Matchmaker
> matchmaker #!5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
beta_no1_cl3_rsr_real_space_refined.cif, chain 2 (#5), sequence alignment
score = 7217
RMSD between 1724 pruned atom pairs is 0.864 angstroms; (across all 1798
pairs: 0.987)
> matchmaker #!5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
beta_no1_cl3_rsr_real_space_refined.cif, chain 2 (#5), sequence alignment
score = 7217
RMSD between 1724 pruned atom pairs is 0.864 angstroms; (across all 1798
pairs: 0.987)
> cartoon style width 1 thickness 1
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/6gsm.cif"
6gsm.cif title:
Structure of a partial yeast 48S preinitiation complex in open conformation.
[more info...]
Chain information for 6gsm.cif #6
---
Chain | Description | UniProt
1 | Met-tRNAi |
2 | 18S ribosomal RNA |
3 | mRNA (5'-R(P*AP*AP*U)-3') |
A | 40S ribosomal protein S0 | RSSA_KLULA
B | 40S ribosomal protein S1 | RS3A_KLULA
C | KLLA0F09812p | Q6CKL3_KLULA
D | KLLA0D08305p | Q6CRK7_KLULA
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA
F | KLLA0D10659p | Q6CRA3_KLULA
G | 40S ribosomal protein S6 | RS6_KLULA
H | 40S ribosomal protein S7 | Q6CTD6_KLULA
I | 40S ribosomal protein S8 | Q6CMG3_KLULA
J | KLLA0E23673p | Q6CM18_KLULA
K | KLLA0B08173p | Q6CVZ5_KLULA
L | KLLA0A10483p | Q6CX80_KLULA
M | 40S ribosomal protein S12 | Q6CLU4_KLULA
N | KLLA0F18040p | Q6CJK0_KLULA
O | 40S ribosomal protein S14 | RS14_KLULA
P | KLLA0F07843p | Q6CKV4_KLULA
Q | 40S ribosomal protein S16 | RS16_KLULA
R | KLLA0B01474p | Q6CWU3_KLULA
S | KLLA0B01562p | Q6CWT9_KLULA
T | KLLA0A07194p | Q6CXM0_KLULA
U | KLLA0F25542p | Q6CIM1_KLULA
V | 40S ribosomal protein S21 | RS21_KLULA
W | 40S ribosomal protein S22 | RS22_KLULA
X | KLLA0B11231p | F2Z602_KLULA
Y | 40S ribosomal protein S24 | Q6CU44_KLULA
Z | KLLA0B06182p | Q6CW78_KLULA
a | 40S ribosomal protein S26 | Q6CS01_KLULA
b | 40S ribosomal protein S27 | Q6CNL2_KLULA
c | 40S ribosomal protein S28 | RS28_KLULA
d | 40S ribosomal protein S29 | RS29_KLULA
e | 40S ribosomal protein S30 | Q6CUH5_KLULA
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA
g | KLLA0E12277p | Q6CNI7_KLULA
h | 60S ribosomal protein L41-A | RL41A_YEAST
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAST
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAST
Non-standard residues in 6gsm.cif #6
---
7NO —
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2~{S})-2-azanyl-4-methylsulfanyl-butanoate
GCP — phosphomethylphosphonic acid guanylate ester
MG — magnesium ion
ZN — zinc ion
> show #!3,6 cartoons
> hide #!3,6 atoms
> close #1
> close #4
> color #6 #ff55ffff
> ui tool show Matchmaker
> matchmaker #!6 to #2/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#2) with 6gsm.cif, chain 2
(#6), sequence alignment score = 7082
RMSD between 1127 pruned atom pairs is 1.049 angstroms; (across all 1780
pairs: 6.002)
> matchmaker #!6 to #2/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#2) with 6gsm.cif, chain 2
(#6), sequence alignment score = 7082
RMSD between 1127 pruned atom pairs is 1.049 angstroms; (across all 1780
pairs: 6.002)
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 276479 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #!3 models
> show #!3 models
> hide #!3,6 atoms
> show #!5 models
> show #!3,5-6 atoms
> hide #!3,5-6 atoms
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF5_displayed_rsr_real_space_refined.cif"
Summary of feedback from opening D:/PhD common folder/OneDrive - Indian
Institute of
Science/Jose_TH_43S_PIC/New_RSR_models/eIF5_displayed_rsr_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 3872
Missing entity information. Treating each chain as a separate entity.
Missing first residue in struct_conn "C00001"
Missing first residue in struct_conn "C00002"
Missing first residue in struct_conn "C00003"
Missing first residue in struct_conn "C00004"
Missing first residue in struct_conn "C00005"
2838 messages similar to the above omitted
Invalid residue range for struct_conf "17": invalid entity "C", near line 275
Invalid residue range for struct_conf "18": invalid entity "C", near line 276
Invalid residue range for struct_conf "19": invalid entity "C", near line 277
Invalid residue range for struct_conf "20": invalid entity "C", near line 278
Invalid residue range for struct_conf "21": invalid entity "C", near line 279
157 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "F 1": invalid entity "C", near
line 3540
Invalid sheet range for struct_sheet_range "F 2": invalid entity "C", near
line 3541
Invalid sheet range for struct_sheet_range "F 3": invalid entity "C", near
line 3542
Invalid sheet range for struct_sheet_range "F 4": invalid entity "C", near
line 3543
Invalid sheet range for struct_sheet_range "G 1": invalid entity "C", near
line 3544
177 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 91304
Skipping chem_comp category: Missing column 'type' near line 91583
Skipping chem_comp category: Missing column 'type' near line 91844
Skipping chem_comp category: Missing column 'type' near line 92129
Skipping chem_comp category: Missing column 'type' near line 92347
15 messages similar to the above omitted
Chain information for eIF5_displayed_rsr_real_space_refined.cif #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
> show #!1,3,5-6 cartoons
> hide #!1,3,5-6 atoms
> color #1 lime
> ui tool show Matchmaker
> matchmaker #!2 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#2), sequence alignment score = 6775.8
RMSD between 1673 pruned atom pairs is 0.858 angstroms; (across all 1780
pairs: 1.400)
> matchmaker #!3 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
beta_no1_cl2_rsr_real_space_refined.cif, chain 2 (#3), sequence alignment
score = 7196
RMSD between 1736 pruned atom pairs is 0.842 angstroms; (across all 1798
pairs: 0.948)
> matchmaker #!5 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
beta_no1_cl3_rsr_real_space_refined.cif, chain 2 (#5), sequence alignment
score = 7217
RMSD between 1724 pruned atom pairs is 0.864 angstroms; (across all 1798
pairs: 0.987)
> matchmaker #!6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
6gsm.cif, chain 2 (#6), sequence alignment score = 6878.8
RMSD between 1140 pruned atom pairs is 1.126 angstroms; (across all 1798
pairs: 5.898)
> matchmaker #!6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
6gsm.cif, chain 2 (#6), sequence alignment score = 6878.8
RMSD between 1140 pruned atom pairs is 1.126 angstroms; (across all 1798
pairs: 5.898)
> matchmaker #!6 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
6gsm.cif, chain 2 (#6), sequence alignment score = 6878.8
RMSD between 1140 pruned atom pairs is 1.126 angstroms; (across all 1798
pairs: 5.898)
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 86963 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/6gsn.cif"
6gsn.cif title:
Structure of a partial yeast 48S preinitiation complex in closed conformation
[more info...]
Chain information for 6gsn.cif #4
---
Chain | Description | UniProt
1 | tRNAi (75-MER) |
2 | 18S rRNA (1798-MER) |
3 | mRNA |
A | 40S ribosomal protein S0 | RSSA_KLULA
B | 40S ribosomal protein S1 | RS3A_KLULA
C | KLLA0F09812p | Q6CKL3_KLULA
D | KLLA0D08305p | Q6CRK7_KLULA
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA
F | KLLA0D10659p | Q6CRA3_KLULA
G | 40S ribosomal protein S6 | RS6_KLULA
H | 40S ribosomal protein S7 | Q6CTD6_KLULA
I | 40S ribosomal protein S8 | Q6CMG3_KLULA
J | KLLA0E23673p | Q6CM18_KLULA
K | KLLA0B08173p | Q6CVZ5_KLULA
L | KLLA0A10483p | Q6CX80_KLULA
M | 40S ribosomal protein S12 | Q6CLU4_KLULA
N | KLLA0F18040p | Q6CJK0_KLULA
O | 40S ribosomal protein S14 | RS14_KLULA
P | KLLA0F07843p | Q6CKV4_KLULA
Q | 40S ribosomal protein S16 | RS16_KLULA
R | KLLA0B01474p | Q6CWU3_KLULA
S | KLLA0B01562p | Q6CWT9_KLULA
T | KLLA0A07194p | Q6CXM0_KLULA
U | KLLA0F25542p | Q6CIM1_KLULA
V | 40S ribosomal protein S21 | RS21_KLULA
W | 40S ribosomal protein S22 | RS22_KLULA
X | RPS23 | Q875M3_KLULC
Y | 40S ribosomal protein S24 | Q6CU44_KLULA
Z | KLLA0B06182p | Q6CW78_KLULA
a | 40S ribosomal protein S26 | Q6CS01_KLULA
b | 40S ribosomal protein S27 | Q6CNL2_KLULA
c | 40S ribosomal protein S28 | RS28_KLULA
d | 40S ribosomal protein S29 | RS29_KLULA
e | 40S ribosomal protein S30 | Q6CUH5_KLULA
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA
g | KLLA0E12277p | Q6CNI7_KLULA
h | 60S ribosomal protein L41-A | RL41A_YEAST
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST
o | Eukaryotic translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAS7
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAS7
Non-standard residues in 6gsn.cif #4
---
GCP — phosphomethylphosphonic acid guanylate ester
MET — methionine
MG — magnesium ion
ZN — zinc ion
> show #!1,3-6 cartoons
> hide #!1,3-6 atoms
> color #4 blue
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 103673 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #!4 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
6gsn.cif, chain 2 (#4), sequence alignment score = 7187.8
RMSD between 1593 pruned atom pairs is 1.097 angstroms; (across all 1798
pairs: 1.479)
> matchmaker #!4 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker eIF5_displayed_rsr_real_space_refined.cif, chain 2 (#1) with
6gsn.cif, chain 2 (#4), sequence alignment score = 7187.8
RMSD between 1593 pruned atom pairs is 1.097 angstroms; (across all 1798
pairs: 1.479)
> hide atoms
> hide #!6 models
> hide #!4 models
> hide #!2 models
> hide #!5 models
> hide #!3 models
> hide #!1 models
> show #!6 models
> select #6/l:220
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true color #000000 dashes 8
> radius 0.015 reveal true
3 contacts
> select clear
> show #!3 models
> hide #7 models
> hide #!6 models
> close #7
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/open_closed_pdbs.cxs"
——— End of log from Wed May 3 14:24:59 2023 ———
opened ChimeraX session
> select #3/1:46
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1828 bonds, 75 residues, 1 model selected
> select #3/1:10
24 atoms, 26 bonds, 1 residue, 1 model selected
> show sel target ab
> cartoon hide sel
> hide sel target a
> cartoon sel
> select clear
> select #3/3:40
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> color sel red
> select clear
> select #3/1:46
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1828 bonds, 75 residues, 1 model selected
> color sel cornflower blue
> select clear
> show #!5 models
> color #5 #aaaa7fff
> show #!4 models
> hide #!4 models
> show #!6 models
> select #6/3:30
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
64 atoms, 71 bonds, 3 residues, 1 model selected
> select up
103158 atoms, 108903 bonds, 10015 residues, 1 model selected
> select down
64 atoms, 71 bonds, 3 residues, 1 model selected
> hide #!6 models
> show #!2 models
> select #2/3:19
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
639 atoms, 709 bonds, 31 residues, 1 model selected
> hide #!5 models
> hide #!2 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> select #4/m:25
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3/l:199
20 atoms, 19 bonds, 2 residues, 2 models selected
> show sel target ab
> select #3/l:197
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> ui tool show Distances
> select #3/l:197@CB
1 atom, 1 residue, 1 model selected
> select add #4/m:25@OH
2 atoms, 2 residues, 2 models selected
> distance #3/l:197@CB #4/m:25@OH
Distance between beta_no1_cl2_rsr_real_space_refined.cif #3/l ALA 197 CB and
6gsn.cif #4/m TYR 25 OH: 1.360Å
> select clear
> hide #!4 models
> select #3/j:52
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #3/j:209
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
2145 atoms, 2177 bonds, 267 residues, 1 model selected
> select clear
> show #!4 models
> color #4 #ff55ffff
> color #6 #5500ffff
> show #!2 models
> close #7
> hide #!2 models
> hide #!4 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/beta_and1_closed_rsr_real_space_refined.cif"
Summary of feedback from opening D:/PhD common folder/OneDrive - Indian
Institute of
Science/Jose_TH_43S_PIC/New_RSR_models/beta_and1_closed_rsr_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 3942
Missing entity information. Treating each chain as a separate entity.
Missing first residue in struct_conn "C00001"
Missing first residue in struct_conn "C00002"
Missing first residue in struct_conn "C00003"
Missing first residue in struct_conn "C00004"
Missing first residue in struct_conn "C00005"
2865 messages similar to the above omitted
Invalid residue range for struct_conf "18": invalid entity "C", near line 276
Invalid residue range for struct_conf "19": invalid entity "C", near line 277
Invalid residue range for struct_conf "20": invalid entity "C", near line 278
Invalid residue range for struct_conf "21": invalid entity "C", near line 279
Invalid residue range for struct_conf "22": invalid entity "C", near line 280
163 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "F 1": invalid entity "C", near
line 3588
Invalid sheet range for struct_sheet_range "F 2": invalid entity "C", near
line 3589
Invalid sheet range for struct_sheet_range "F 3": invalid entity "C", near
line 3590
Invalid sheet range for struct_sheet_range "F 4": invalid entity "C", near
line 3591
Invalid sheet range for struct_sheet_range "G 1": invalid entity "C", near
line 3592
189 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 91586
Skipping chem_comp category: Missing column 'type' near line 91865
Skipping chem_comp category: Missing column 'type' near line 92126
Skipping chem_comp category: Missing column 'type' near line 92411
Skipping chem_comp category: Missing column 'type' near line 92629
15 messages similar to the above omitted
Chain information for beta_and1_closed_rsr_real_space_refined.cif #7
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
> show #!3,7 cartoons
> hide #!3,7 atoms
> cartoon style width 1 thickness 1
> color #7 #ffaa7fff
> show #!4 models
> show #!2 models
> hide #!3 models
> select #4/p:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
50 atoms, 49 bonds, 6 residues, 1 model selected
> select up
4682 atoms, 4811 bonds, 593 residues, 1 model selected
> select up
4690 atoms, 4818 bonds, 594 residues, 1 model selected
> select down
4682 atoms, 4811 bonds, 593 residues, 1 model selected
> select down
50 atoms, 49 bonds, 6 residues, 1 model selected
> select up
4682 atoms, 4811 bonds, 593 residues, 1 model selected
> select down
50 atoms, 49 bonds, 6 residues, 1 model selected
> select clear
> select #4/p:232
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
55 atoms, 57 bonds, 6 residues, 1 model selected
> select up
4682 atoms, 4811 bonds, 593 residues, 1 model selected
> cartoon hide sel
> select #4/p:728
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
212 atoms, 214 bonds, 24 residues, 1 model selected
> select up
292 atoms, 298 bonds, 33 residues, 1 model selected
> select up
401 atoms, 407 bonds, 53 residues, 1 model selected
> select up
465 atoms, 471 bonds, 65 residues, 1 model selected
> select up
501 atoms, 508 bonds, 69 residues, 1 model selected
> select up
5147 atoms, 5282 bonds, 658 residues, 1 model selected
> select up
103798 atoms, 109571 bonds, 10079 residues, 1 model selected
> select down
5147 atoms, 5282 bonds, 658 residues, 1 model selected
> cartoon hide sel
> select #4/s:129
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 9 residues, 1 model selected
> select up
2019 atoms, 2064 bonds, 258 residues, 1 model selected
> cartoon hide sel
> select #4/r:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
49 atoms, 48 bonds, 6 residues, 1 model selected
> select up
392 atoms, 399 bonds, 49 residues, 1 model selected
> select up
103798 atoms, 109571 bonds, 10079 residues, 1 model selected
> select down
392 atoms, 399 bonds, 49 residues, 1 model selected
> cartoon hide sel
> select #4/s:276
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
69 atoms, 72 bonds, 7 residues, 1 model selected
> select up
587 atoms, 605 bonds, 72 residues, 1 model selected
> cartoon hide sel
> select clear
> hide #!4 models
> hide #!7 models
> show #!3 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/Maps/betaNO1_cl2_gauss134.mrc"
Opened betaNO1_cl2_gauss134.mrc as #8, grid size 300,300,300, pixel 1.34,
shown at level 0.0693, step 2, values float32
> hide #!2 models
> volume #8 step 1
> volume #8 level 0.02
> ui tool show "Hide Dust"
> surface dust #8 size 35
> volume #8 style mesh
> volume #8 level 0.015
> show #!2 models
> hide #!8 models
> show #!4 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!8 models
> volume #8 level 0.025
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!5 models
> color #5 #ffaa00ff
> close #7
> select #3/1:57
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1828 bonds, 75 residues, 1 model selected
> color sel yellow
> select clear
> select #5/3:40
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> color sel red
> select clear
> show #!8 models
> volume #8 level 0.015
> volume #8 level 0.013
> hide #!5 models
> hide #!8 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #3/3:39
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> color sel yellow
> select clear
> color #3 #ffaa00ff
> show #!8 models
> ui tool show "Color Zone"
> color zone #8 near #3 distance 24
> color zone #8 near #3 distance 2
> color zone #8 near #3 distance 28
> color zone #8 near #3 distance 29
> color zone #8 near #3 distance 30
> color zone #8 near #3 distance 31
> color zone #8 near #3 distance 2
> color zone #8 near #3 distance 25
> show #!2 models
> color #2 #ffaa00ff
> color zone #8 near #3 distance 25
> color zone #8 near #2 distance 25
> color zone #8 near #2 distance 26
> color zone #8 near #2 distance 27
> color zone #8 near #2 distance 28
> color zone #8 near #2 distance 29
> color zone #8 near #2 distance 30
> color zone #8 near #2 distance 31
> color zone #8 near #2 distance 32
> hide #!2 models
> transparency #3,8 40
> transparency #3,8 60
> transparency #3,8 20
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/5me7.pdb"
5me7.pdb title:
Crystal structure of EIF4E from C. Melo [more info...]
Chain information for 5me7.pdb #7
---
Chain | Description | UniProt
A B C D | eukaryotic translation initiation factor 4E | Q00LS8_CUCME
Non-standard residues in 5me7.pdb #7
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> ui mousemode right "translate selected models"
> select add #7
5880 atoms, 5920 bonds, 4 pseudobonds, 850 residues, 2 models selected
> view matrix models #7,1,0,0,278.12,0,1,0,112.75,0,0,1,233.29
> view matrix models #7,1,0,0,298.45,0,1,0,61.77,0,0,1,268.43
> select clear
> select #7/C:95
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
83 atoms, 86 bonds, 9 residues, 1 model selected
> select up
1400 atoms, 1447 bonds, 174 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/D:99
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
83 atoms, 86 bonds, 9 residues, 1 model selected
> select up
1217 atoms, 1253 bonds, 150 residues, 1 model selected
> select up
1232 atoms, 1268 bonds, 152 residues, 1 model selected
> select up
1409 atoms, 1456 bonds, 173 residues, 1 model selected
> select up
1417 atoms, 1456 bonds, 181 residues, 1 model selected
> select up
4480 atoms, 4473 bonds, 676 residues, 1 model selected
> select down
1417 atoms, 1456 bonds, 181 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/B:139
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
67 atoms, 70 bonds, 8 residues, 1 model selected
> select up
1228 atoms, 1264 bonds, 151 residues, 1 model selected
> select up
1248 atoms, 1284 bonds, 154 residues, 1 model selected
> select up
1415 atoms, 1462 bonds, 173 residues, 1 model selected
> select up
1467 atoms, 1467 bonds, 220 residues, 1 model selected
> select up
3063 atoms, 3017 bonds, 495 residues, 1 model selected
> select down
1467 atoms, 1467 bonds, 220 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 24 atoms, 8 residues, 19 bonds
> delete atoms sel
> delete bonds sel
> select #7/A:216
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> select up
1244 atoms, 1279 bonds, 154 residues, 1 model selected
> select down
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> view matrix models #7,1,0,0,263.31,0,1,0,160.98,0,0,1,184.39
> view matrix models #7,1,0,0,287.53,0,1,0,160.75,0,0,1,171.97
> view matrix models #7,1,0,0,279.84,0,1,0,157.82,0,0,1,173.08
> view matrix models #7,1,0,0,276.44,0,1,0,181.71,0,0,1,163.7
> view matrix models #7,1,0,0,276.48,0,1,0,180.68,0,0,1,158.8
> view matrix models
> #7,0.99577,0.090799,-0.014211,275.77,-0.071991,0.86675,0.49351,187.06,0.057128,-0.4904,0.86962,160.34
> view matrix models
> #7,0.9912,0.12788,0.034293,276.16,-0.1129,0.68109,0.72344,190.59,0.069155,-0.72095,0.68953,159.3
> color zone #8 near #7 distance 20
> select clear
> select #7/A:92
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
69 atoms, 71 bonds, 8 residues, 1 model selected
> select up
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> select up
1244 atoms, 1279 bonds, 154 residues, 1 model selected
> select up
1424 atoms, 1470 bonds, 175 residues, 1 model selected
> select up
1472 atoms, 1475 bonds, 218 residues, 1 model selected
> select up
1517 atoms, 1475 bonds, 263 residues, 1 model selected
> select down
1472 atoms, 1475 bonds, 218 residues, 1 model selected
> color sel gray
> color zone #8 near #7 distance 20
> select clear
> select #7/A:217
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> select up
1244 atoms, 1279 bonds, 154 residues, 1 model selected
> select up
1424 atoms, 1470 bonds, 175 residues, 1 model selected
> view matrix models
> #7,0.9912,0.12788,0.034293,278.89,-0.1129,0.68109,0.72344,189.06,0.069155,-0.72095,0.68953,153.51
> view matrix models
> #7,0.99568,0.055134,-0.074675,277.87,-0.031308,0.95682,0.28899,182.84,0.087384,-0.28541,0.95441,155
> view matrix models
> #7,0.64337,0.013793,0.76544,284.87,-0.15033,0.98265,0.10865,178.79,-0.75065,-0.18497,0.63427,139.64
> view matrix models
> #7,0.60762,-0.29169,0.73873,285.67,-0.70818,0.22209,0.67019,183.26,-0.35955,-0.93037,-0.071618,139.04
> view matrix models
> #7,0.71998,-0.41535,0.55598,285.29,-0.69382,-0.41286,0.59005,185.7,-0.015532,-0.81058,-0.58543,135.88
> view matrix models
> #7,0.85578,-0.34009,0.38985,284.38,-0.45218,-0.85782,0.24428,186.45,0.25135,-0.38533,-0.88789,132.97
> view matrix models
> #7,0.85578,-0.34009,0.38985,279.9,-0.45218,-0.85782,0.24428,185.74,0.25135,-0.38533,-0.88789,126.31
> view matrix models
> #7,0.50736,-0.71755,0.47718,278.66,-0.74473,-0.64371,-0.17613,175.31,0.43355,-0.26601,-0.86097,128.34
> view matrix models
> #7,0.24804,-0.86628,0.43363,275.6,-0.81508,-0.42854,-0.38987,170.45,0.52356,-0.25675,-0.81238,130.07
> view matrix models
> #7,0.14864,-0.90636,0.3955,274.04,-0.80308,-0.34401,-0.48654,168.86,0.57703,-0.2453,-0.77901,131.13
> color zone #8 near #7 distance 20
> view matrix models
> #7,0.14864,-0.90636,0.3955,273.66,-0.80308,-0.34401,-0.48654,167.55,0.57703,-0.2453,-0.77901,128
> color zone #8 near #7 distance 20
> select down
1244 atoms, 1279 bonds, 154 residues, 1 model selected
> color zone #8 near #7 distance 20
> select down
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> select down
42 atoms, 43 bonds, 5 residues, 1 model selected
> select up
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> color zone #8 near #7 distance 20
> color zone #8 near #7 distance 2
> color zone #8 near #7 distance 10
> select clear
> show #!2 models
> color zone #8 near #2 distance 10
> color zone #8 near #2 distance 2
> color zone #8 near #2 distance 25
> color zone #8 near #2 distance 2
> color zone #8 near #2 distance 28
> color zone #8 near #2 distance 2
> color zone #8 near #2 distance 3
> color zone #8 near #2 distance 30
> color zone #8 near #2 distance 2
> color zone #8 near #2 distance 25
> select #7/A:53
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
39 atoms, 38 bonds, 6 residues, 1 model selected
> select up
190 atoms, 200 bonds, 23 residues, 1 model selected
> select up
209 atoms, 218 bonds, 26 residues, 1 model selected
> select up
1424 atoms, 1470 bonds, 175 residues, 1 model selected
> select down
209 atoms, 218 bonds, 26 residues, 1 model selected
> select up
1424 atoms, 1470 bonds, 175 residues, 1 model selected
> view matrix models
> #7,0.14864,-0.90636,0.3955,314.7,-0.80308,-0.34401,-0.48654,152.67,0.57703,-0.2453,-0.77901,127.21
> view matrix models
> #7,0.14864,-0.90636,0.3955,304.11,-0.80308,-0.34401,-0.48654,123.66,0.57703,-0.2453,-0.77901,159.22
> color sel orange
> color zone #8 near #7 distance 25
> view matrix models
> #7,0.14864,-0.90636,0.3955,357.16,-0.80308,-0.34401,-0.48654,101.31,0.57703,-0.2453,-0.77901,145.36
> color zone #8 near #2 distance 25
> view matrix models
> #7,0.14864,-0.90636,0.3955,275.09,-0.80308,-0.34401,-0.48654,107.52,0.57703,-0.2453,-0.77901,140.71
> view matrix models
> #7,0.14864,-0.90636,0.3955,266.63,-0.80308,-0.34401,-0.48654,152.06,0.57703,-0.2453,-0.77901,150.04
> view matrix models
> #7,0.14864,-0.90636,0.3955,270.51,-0.80308,-0.34401,-0.48654,148.75,0.57703,-0.2453,-0.77901,131.9
> view matrix models
> #7,0.14864,-0.90636,0.3955,273.5,-0.80308,-0.34401,-0.48654,165.94,0.57703,-0.2453,-0.77901,133.33
> view matrix models
> #7,0.14864,-0.90636,0.3955,267.99,-0.80308,-0.34401,-0.48654,163.14,0.57703,-0.2453,-0.77901,124.23
> color sel gray
> select clear
> color zone #8 near #7 distance 25
> color #8 #ffaa00ff models
> color zone #8 near #7 distance 25
> color zone #8 near #7 distance 10
[Repeated 1 time(s)]
> select #7/A:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
26 atoms, 26 bonds, 3 residues, 1 model selected
> select up
1234 atoms, 1270 bonds, 152 residues, 1 model selected
> select up
1244 atoms, 1279 bonds, 154 residues, 1 model selected
> view matrix models
> #7,0.14864,-0.90636,0.3955,319.86,-0.80308,-0.34401,-0.48654,134.34,0.57703,-0.2453,-0.77901,80.262
> select clear
Drag select of 46 residues
> delete atoms sel
> delete bonds sel
> color #8 #55aa00ff models
> color #8 #ffaa00ff models
> select #7/A:187
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
69 atoms, 70 bonds, 8 residues, 1 model selected
> select up
531 atoms, 542 bonds, 66 residues, 1 model selected
> view matrix models
> #7,0.14864,-0.90636,0.3955,275.11,-0.80308,-0.34401,-0.48654,150.29,0.57703,-0.2453,-0.77901,130.68
> view matrix models
> #7,0.14864,-0.90636,0.3955,269.96,-0.80308,-0.34401,-0.48654,144.79,0.57703,-0.2453,-0.77901,122.08
> view matrix models
> #7,0.14864,-0.90636,0.3955,270.67,-0.80308,-0.34401,-0.48654,145.31,0.57703,-0.2453,-0.77901,122.68
> view matrix models
> #7,0.14864,-0.90636,0.3955,269.29,-0.80308,-0.34401,-0.48654,149.55,0.57703,-0.2453,-0.77901,124.77
> view matrix models
> #7,0.14864,-0.90636,0.3955,273.3,-0.80308,-0.34401,-0.48654,149.62,0.57703,-0.2453,-0.77901,124.97
> view matrix models
> #7,0.14864,-0.90636,0.3955,276.63,-0.80308,-0.34401,-0.48654,152.19,0.57703,-0.2453,-0.77901,125.91
> view matrix models
> #7,0.23696,-0.87454,0.42311,278.34,-0.73634,-0.44578,-0.509,152.54,0.63376,-0.19094,-0.7496,127.26
> view matrix models
> #7,0.23696,-0.87454,0.42311,271.76,-0.73634,-0.44578,-0.509,149.71,0.63376,-0.19094,-0.7496,123.64
> view matrix models
> #7,0.066579,-0.92269,0.37975,268.67,-0.81021,-0.27212,-0.51914,148.56,0.58234,-0.27311,-0.76569,122.65
> view matrix models
> #7,-0.085372,-0.93606,0.34131,265.93,-0.85181,-0.10913,-0.51235,148.17,0.51684,-0.33448,-0.78803,121.34
> view matrix models
> #7,-0.27984,-0.91372,0.29462,262.46,-0.90601,0.14984,-0.39585,150.02,0.31755,-0.3777,-0.86977,117.06
> color zone #8 near #7 distance 10
> close #7
> color #8 #ffaa7fff models
> color #8 #ffaa00ff models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/5me7.pdb"
5me7.pdb title:
Alphafold monomer V2.0 prediction for eukaryotic translation initiation factor
4E-binding protein 2 (Q13542) [more info...]
Chain information for 5me7.pdb #7
---
Chain | Description | UniProt
A | eukaryotic translation initiation factor 4E-binding protein 2 |
4EBP2_HUMAN
> select #7/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 5 residues, 1 model selected
> select up
907 atoms, 927 bonds, 120 residues, 1 model selected
> view matrix models #7,1,0,0,326.15,0,1,0,245.39,0,0,1,55.551
> view matrix models #7,1,0,0,280.05,0,1,0,185.61,0,0,1,108.99
> view matrix models #7,1,0,0,281.07,0,1,0,196.63,0,0,1,117.34
> view matrix models #7,1,0,0,267.56,0,1,0,195.57,0,0,1,115.06
> view matrix models
> #7,0.76347,0.56929,-0.30499,268.68,-0.62433,0.77142,-0.12295,190.82,0.16528,0.28428,0.94439,117.32
> view matrix models
> #7,0.25803,0.80117,-0.53995,267,-0.9583,0.28326,-0.037649,186.72,0.12278,0.52715,0.84086,118.21
> view matrix models
> #7,-0.31469,0.65892,-0.68322,262.9,-0.93995,-0.31655,0.12765,183.33,-0.13216,0.68237,0.71896,117.67
> view matrix models
> #7,-0.53413,0.4659,-0.70543,260.48,-0.78037,-0.59265,0.19945,182.06,-0.32515,0.65704,0.68013,116.58
> view matrix models
> #7,-0.65358,0.26249,-0.70988,258.38,-0.55624,-0.80264,0.21533,180.91,-0.51325,0.5356,0.6706,114.99
> view matrix models
> #7,-0.6545,0.29628,-0.69559,258.83,-0.18615,-0.95485,-0.23156,175.57,-0.73279,-0.022067,0.6801,109.73
> view matrix models
> #7,-0.6545,0.29628,-0.69559,269.75,-0.18615,-0.95485,-0.23156,176.03,-0.73279,-0.022067,0.6801,110.43
> view matrix models
> #7,-0.8358,0.33162,-0.43758,272.45,-0.3065,-0.94305,-0.12927,176.97,-0.45553,0.026078,0.88984,113.76
> view matrix models
> #7,-0.8358,0.33162,-0.43758,274.8,-0.3065,-0.94305,-0.12927,169.51,-0.45553,0.026078,0.88984,103.95
> view matrix models
> #7,-0.8358,0.33162,-0.43758,268.11,-0.3065,-0.94305,-0.12927,157.07,-0.45553,0.026078,0.88984,118.77
> view matrix models
> #7,-0.8358,0.33162,-0.43758,266.12,-0.3065,-0.94305,-0.12927,158.81,-0.45553,0.026078,0.88984,119.61
> color sel gray
> color zone #8 near #7 distance 10
> view matrix models
> #7,-0.8358,0.33162,-0.43758,263.51,-0.3065,-0.94305,-0.12927,159.6,-0.45553,0.026078,0.88984,116.84
> color zone #8 near #7 distance 10
> view matrix models
> #7,-0.8358,0.33162,-0.43758,262.07,-0.3065,-0.94305,-0.12927,159.11,-0.45553,0.026078,0.88984,115.95
> color zone #8 near #7 distance 10
> hide #7 models
> show #7 models
> view matrix models
> #7,-0.8358,0.33162,-0.43758,308.02,-0.3065,-0.94305,-0.12927,242.9,-0.45553,0.026078,0.88984,202.67
> view matrix models
> #7,-0.82274,-0.3136,-0.47408,302.02,0.30377,-0.94752,0.099612,246.73,-0.48044,-0.062054,0.87483,201.68
> view matrix models
> #7,-0.7845,-0.39293,-0.47976,301.35,0.27784,-0.91435,0.29456,249.08,-0.55441,0.097782,0.82648,202.38
> view matrix models
> #7,-0.7845,-0.39293,-0.47976,301.25,0.27784,-0.91435,0.29456,231.74,-0.55441,0.097782,0.82648,204.48
> color zone #8 near #7 distance 10
> hide #7 models
> show #7 models
> view matrix models
> #7,-0.7845,-0.39293,-0.47976,299.36,0.27784,-0.91435,0.29456,236.22,-0.55441,0.097782,0.82648,201.3
> color zone #8 near #7 distance 10
> hide #7 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/5me7.pdb"
5me7.pdb title:
Alphafold monomer V2.0 prediction for eukaryotic translation initiation factor
4E-binding protein 2 (Q13542) [more info...]
Chain information for 5me7.pdb #9
---
Chain | Description | UniProt
A | eukaryotic translation initiation factor 4E-binding protein 2 |
4EBP2_HUMAN
> select clear
> select #9/A:20
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
37 atoms, 36 bonds, 5 residues, 1 model selected
> select up
907 atoms, 927 bonds, 120 residues, 1 model selected
> view matrix models #9,1,0,0,341.91,0,1,0,205.08,0,0,1,87.373
> view matrix models #9,1,0,0,299.75,0,1,0,230.01,0,0,1,114
> view matrix models #9,1,0,0,305.24,0,1,0,235.26,0,0,1,135.86
> view matrix models #9,1,0,0,270.72,0,1,0,204.67,0,0,1,100.8
> view matrix models #9,1,0,0,268.07,0,1,0,202.86,0,0,1,110.44
> color sel dark gray
> color sel gray
> color zone #8 near #9 distance 10
> view matrix models #9,1,0,0,275.52,0,1,0,202.52,0,0,1,113.94
> color zone #8 near #9 distance 10
> view matrix models #9,1,0,0,278.11,0,1,0,216.96,0,0,1,121.23
> color zone #8 near #9 distance 10
> view matrix models #9,1,0,0,271.52,0,1,0,208.42,0,0,1,118.96
> view matrix models #9,1,0,0,279.89,0,1,0,207.64,0,0,1,121.49
> view matrix models #9,1,0,0,275.27,0,1,0,208.61,0,0,1,119.7
> color zone #8 near #9 distance 10
> close #9
> show #7 models
> color zone #8 near #7 distance 10
> hide #7 models
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/AF-P69222-F1-model_v4.pdb"
AF-P69222-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for translation initiation factor if-1
(P69222) [more info...]
Chain information for AF-P69222-F1-model_v4.pdb #9
---
Chain | Description | UniProt
A | translation initiation factor if-1 | IF1_ECOLI
> select add #9
577 atoms, 584 bonds, 72 residues, 1 model selected
> view matrix models #9,1,0,0,310.57,0,1,0,177.94,0,0,1,250.53
> view matrix models #9,1,0,0,239.55,0,1,0,195.38,0,0,1,185.32
> view matrix models #9,1,0,0,241.55,0,1,0,169.48,0,0,1,180.9
> view matrix models #9,1,0,0,273.4,0,1,0,189.28,0,0,1,186.03
> view matrix models #9,1,0,0,266.74,0,1,0,185.68,0,0,1,149.01
> view matrix models #9,1,0,0,267.81,0,1,0,178.65,0,0,1,140.93
> view matrix models #9,1,0,0,262.24,0,1,0,178.52,0,0,1,143.53
> color sel gray
> show #7 models
> select add #7/A:68
582 atoms, 588 bonds, 73 residues, 2 models selected
> select up
606 atoms, 613 bonds, 76 residues, 2 models selected
> select up
1484 atoms, 1511 bonds, 192 residues, 2 models selected
> color zone #8 near #9 distance 10
> view matrix models
> #7,-0.7845,-0.39293,-0.47976,300.37,0.27784,-0.91435,0.29456,235.73,-0.55441,0.097782,0.82648,199.71,#9,1,0,0,263.25,0,1,0,178.03,0,0,1,141.94
> color zone #8 near #9 distance 10
> view matrix models
> #7,-0.7845,-0.39293,-0.47976,301.81,0.27784,-0.91435,0.29456,235.77,-0.55441,0.097782,0.82648,199.74,#9,1,0,0,264.69,0,1,0,178.07,0,0,1,141.97
> color zone #8 near #9 distance 10
> color zone #8 near sel distance 10
> select clear
> hide #9 models
> hide #7 models
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> hide #!2 models
> transparency #3,8 50
> transparency #3,8 40
> transparency #3,8 60
> hide #!3 models
> transparency #8 20
> transparency #8 100
> transparency #8 80
> transparency #8 0
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> transparency #8 20
> transparency #8 40
> volume #8
> volume #8 style surface
> transparency #8 0
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting full
> graphics silhouettes false
> lighting shadows false
> save C:\ProgramData\ChimeraX\image75.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF5_CTD.cxs"
> close #8
> close #9
> close #7
> color #2 cyan
> show #!3 models
> lighting soft
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting flat
> lighting soft
> show #!2 models
> hide #!3 models
> show #!5 models
> licorice scale #2 2
Unknown command: licorice scale #2 2
> licorice scale #2 2.0
Unknown command: licorice scale #2 2.0
> licorice scale #5 2.0
Unknown command: licorice scale #5 2.0
> repr wireframe #5 radius 0.2
Unknown command: repr wireframe #5 radius 0.2
> select add #5
86904 atoms, 92314 bonds, 11 pseudobonds, 7914 residues, 2 models selected
> repr wireframe sel and bonds #5 color AtomRadius
Unknown command: repr wireframe sel and bonds #5 color AtomRadius
> repr wireframe #5 radius 0.2
Unknown command: repr wireframe #5 radius 0.2
> select clear
> hide #!2 models
> show #!2 models
> select #5/l:158
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select up
86904 atoms, 92314 bonds, 7914 residues, 1 model selected
> select add #2/m:12
86911 atoms, 92321 bonds, 7915 residues, 2 models selected
> select up
87065 atoms, 92481 bonds, 7933 residues, 2 models selected
> select up
88044 atoms, 93478 bonds, 8061 residues, 2 models selected
> select ~sel
484110 atoms, 512167 bonds, 3389 pseudobonds, 45964 residues, 14 models
selected
> cartoon hide (#!2 & sel)
> select #5/l:161
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select up
86904 atoms, 92314 bonds, 7914 residues, 1 model selected
> select down
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel medium violet red
> color sel medium orchid
> select #5/i:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> select up
86904 atoms, 92314 bonds, 7914 residues, 1 model selected
> select down
764 atoms, 773 bonds, 95 residues, 1 model selected
> color sel red
> select #5/3:34
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> color sel blue
> select clear
> lighting full
> lighting flat
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> set bgColor white
> select #5/i:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> select add #5/l:183
773 atoms, 781 bonds, 96 residues, 1 model selected
> select up
1847 atoms, 1872 bonds, 229 residues, 1 model selected
> select add #2/m:12
1854 atoms, 1879 bonds, 230 residues, 2 models selected
> select up
2008 atoms, 2039 bonds, 248 residues, 2 models selected
> select up
2987 atoms, 3036 bonds, 376 residues, 2 models selected
> view sel
> select clear
> save C:\ProgramData\ChimeraX\image76.png supersample 3
> view
> show #!3 models
> hide #!5 models
> show #!5 models
> select #2/m:12
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> cartoon #2-3,5
> select #2/l:164
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
124 atoms, 126 bonds, 15 residues, 1 model selected
> select up
546 atoms, 558 bonds, 68 residues, 1 model selected
> select up
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select up
104236 atoms, 109970 bonds, 10152 residues, 1 model selected
> select down
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select ~sel
571117 atoms, 604594 bonds, 3397 pseudobonds, 53896 residues, 16 models
selected
> cartoon hide (#!2-3,5 & sel)
> cartoon (#!2-3,5 & sel)
> select clear
> hide #!3 models
> hide #!5 models
> select #2/l:164
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
124 atoms, 126 bonds, 15 residues, 1 model selected
> select up
546 atoms, 558 bonds, 68 residues, 1 model selected
> select up
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select up
104236 atoms, 109970 bonds, 10152 residues, 1 model selected
> select down
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select ~sel
571117 atoms, 604594 bonds, 3397 pseudobonds, 53896 residues, 16 models
selected
> select subtract #1
483998 atoms, 512055 bonds, 3388 pseudobonds, 45949 residues, 14 models
selected
> select subtract #3
397059 atoms, 419707 bonds, 3376 pseudobonds, 38031 residues, 12 models
selected
> select subtract #4
293261 atoms, 310136 bonds, 1639 pseudobonds, 27952 residues, 8 models
selected
> select subtract #5
206357 atoms, 217822 bonds, 1628 pseudobonds, 20038 residues, 6 models
selected
> select subtract #6
103199 atoms, 108919 bonds, 27 pseudobonds, 10023 residues, 2 models selected
> cartoon hide (#!2 & sel)
> show #!3 models
> show #!5 models
> show #!4 models
> select #4/l:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
31 atoms, 30 bonds, 4 residues, 1 model selected
> select up
383 atoms, 391 bonds, 49 residues, 1 model selected
> select up
438 atoms, 444 bonds, 55 residues, 1 model selected
> select up
872 atoms, 885 bonds, 107 residues, 1 model selected
> select up
1016 atoms, 1030 bonds, 126 residues, 1 model selected
> select up
1017 atoms, 1030 bonds, 127 residues, 1 model selected
> select up
103798 atoms, 109571 bonds, 10079 residues, 1 model selected
> select down
1017 atoms, 1030 bonds, 127 residues, 1 model selected
> select ~sel
571137 atoms, 604615 bonds, 3395 pseudobonds, 53898 residues, 16 models
selected
> select subtract #2
466901 atoms, 494645 bonds, 3365 pseudobonds, 43746 residues, 14 models
selected
> select subtract #3
379962 atoms, 402297 bonds, 3353 pseudobonds, 35828 residues, 12 models
selected
> select subtract #5
293058 atoms, 309983 bonds, 3342 pseudobonds, 27914 residues, 10 models
selected
> select subtract #6
189900 atoms, 201080 bonds, 1741 pseudobonds, 17899 residues, 6 models
selected
> select subtract #1
102781 atoms, 108541 bonds, 1732 pseudobonds, 9952 residues, 4 models selected
> cartoon hide (#!4 & sel)
> select #3/l:159
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select up
86939 atoms, 92348 bonds, 7918 residues, 1 model selected
> select down
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel yellow
> select clear
> select #5/l:227
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> hide #!3 models
> show #!3 models
> select #3/l:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select ~sel
571071 atoms, 604546 bonds, 3397 pseudobonds, 53891 residues, 16 models
selected
> select subtract #2
466835 atoms, 494576 bonds, 3367 pseudobonds, 43739 residues, 14 models
selected
> select subtract #4
363037 atoms, 385005 bonds, 1630 pseudobonds, 33660 residues, 10 models
selected
> select subtract #5
276133 atoms, 292691 bonds, 1619 pseudobonds, 25746 residues, 8 models
selected
> select subtract #6
172975 atoms, 183788 bonds, 18 pseudobonds, 15731 residues, 4 models selected
> select subtract #1
85856 atoms, 91249 bonds, 9 pseudobonds, 7784 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select clear
> select #5/i:106
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> select add #4/l:165
770 atoms, 778 bonds, 96 residues, 2 models selected
> select up
892 atoms, 902 bonds, 111 residues, 2 models selected
> select up
1290 atoms, 1310 bonds, 161 residues, 2 models selected
> select add #5/l:162
1297 atoms, 1317 bonds, 162 residues, 2 models selected
> select up
2393 atoms, 2428 bonds, 297 residues, 2 models selected
> view sel
> select clear
> select #4/l:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
82 atoms, 84 bonds, 9 residues, 1 model selected
> select up
143 atoms, 146 bonds, 17 residues, 1 model selected
> select up
236 atoms, 241 bonds, 29 residues, 1 model selected
> select up
526 atoms, 537 bonds, 66 residues, 1 model selected
> select up
546 atoms, 556 bonds, 68 residues, 1 model selected
> select up
872 atoms, 885 bonds, 107 residues, 1 model selected
> select up
1016 atoms, 1030 bonds, 126 residues, 1 model selected
> select up
1017 atoms, 1030 bonds, 127 residues, 1 model selected
> select down
1016 atoms, 1030 bonds, 126 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> color sel thistle
> color sel pink
> color sel plum
> color sel violet
> color sel plum
> select clear
> save C:\ProgramData\ChimeraX\image77.png supersample 3
> cartoon #2-5
> view
> select add #4
103798 atoms, 109571 bonds, 1737 pseudobonds, 10079 residues, 4 models
selected
> select subtract #4
Nothing selected
> select #4/l:161
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
128 atoms, 129 bonds, 16 residues, 1 model selected
> select up
526 atoms, 537 bonds, 66 residues, 1 model selected
> select up
546 atoms, 556 bonds, 68 residues, 1 model selected
> select up
872 atoms, 885 bonds, 107 residues, 1 model selected
> select up
1016 atoms, 1030 bonds, 126 residues, 1 model selected
> select up
1017 atoms, 1030 bonds, 127 residues, 1 model selected
> select up
103798 atoms, 109571 bonds, 10079 residues, 1 model selected
> select down
1017 atoms, 1030 bonds, 127 residues, 1 model selected
> select add #2/l:163
1024 atoms, 1037 bonds, 128 residues, 2 models selected
> select up
1141 atoms, 1156 bonds, 142 residues, 2 models selected
> select up
1563 atoms, 1588 bonds, 195 residues, 2 models selected
> select up
2054 atoms, 2081 bonds, 256 residues, 2 models selected
> select up
208034 atoms, 219541 bonds, 20231 residues, 2 models selected
> select down
2054 atoms, 2081 bonds, 256 residues, 2 models selected
> select add #3/l:166
2062 atoms, 2088 bonds, 257 residues, 3 models selected
> select up
3137 atoms, 3180 bonds, 390 residues, 3 models selected
> select add #5/l:223
3146 atoms, 3188 bonds, 391 residues, 4 models selected
> select up
4220 atoms, 4279 bonds, 524 residues, 4 models selected
> select up
381877 atoms, 404203 bonds, 36063 residues, 4 models selected
> select up
572154 atoms, 605645 bonds, 54025 residues, 6 models selected
> select down
381877 atoms, 404203 bonds, 36063 residues, 4 models selected
> select down
4220 atoms, 4279 bonds, 524 residues, 4 models selected
> select add #3/i:117
4225 atoms, 4283 bonds, 525 residues, 4 models selected
> select up
5019 atoms, 5086 bonds, 623 residues, 4 models selected
> select up
381877 atoms, 404203 bonds, 36063 residues, 4 models selected
> select ~sel
190277 atoms, 201442 bonds, 1610 pseudobonds, 17962 residues, 6 models
selected
> cartoon hide #2-5
> cartoon #2-5
> select clear
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select #2/l:161
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
124 atoms, 126 bonds, 15 residues, 1 model selected
> select up
546 atoms, 558 bonds, 68 residues, 1 model selected
> select up
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select down
546 atoms, 558 bonds, 68 residues, 1 model selected
> select up
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select up
104236 atoms, 109970 bonds, 10152 residues, 1 model selected
> select down
1037 atoms, 1051 bonds, 129 residues, 1 model selected
> select ~sel
571117 atoms, 604594 bonds, 3397 pseudobonds, 53896 residues, 16 models
selected
> select subtract #3
484178 atoms, 512246 bonds, 3385 pseudobonds, 45978 residues, 14 models
selected
> select subtract #4
380380 atoms, 402675 bonds, 1648 pseudobonds, 35899 residues, 10 models
selected
> select subtract #6
277222 atoms, 293772 bonds, 47 pseudobonds, 25884 residues, 6 models selected
> select subtract #5
190318 atoms, 201458 bonds, 36 pseudobonds, 17970 residues, 4 models selected
> select subtract #1
103199 atoms, 108919 bonds, 27 pseudobonds, 10023 residues, 2 models selected
> cartoon hide (#!2 & sel)
> hide #!2 models
> select add #2
104236 atoms, 109970 bonds, 30 pseudobonds, 10152 residues, 2 models selected
> show #!3 models
> select subtract #2
Nothing selected
> select #3/l:158
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select ~sel
571071 atoms, 604546 bonds, 3397 pseudobonds, 53891 residues, 16 models
selected
> select subtract #1
483952 atoms, 512007 bonds, 3388 pseudobonds, 45944 residues, 14 models
selected
> select subtract #2
379716 atoms, 402037 bonds, 3358 pseudobonds, 35792 residues, 12 models
selected
> select subtract #4
275918 atoms, 292466 bonds, 1621 pseudobonds, 25713 residues, 8 models
selected
> select subtract #5
189014 atoms, 200152 bonds, 1610 pseudobonds, 17799 residues, 6 models
selected
> select subtract #6
85856 atoms, 91249 bonds, 9 pseudobonds, 7784 residues, 2 models selected
> select #4/2
38251 atoms, 42691 bonds, 1630 pseudobonds, 1874 residues, 3 models selected
> cartoon hide #3
> show #!2 models
> select add #3
125190 atoms, 135039 bonds, 1642 pseudobonds, 9792 residues, 5 models selected
> select subtract #3
38251 atoms, 42691 bonds, 1630 pseudobonds, 1874 residues, 3 models selected
> show #!4 models
> select add #3
125190 atoms, 135039 bonds, 1642 pseudobonds, 9792 residues, 5 models selected
> select add #4
190737 atoms, 201919 bonds, 1749 pseudobonds, 17997 residues, 6 models
selected
> select subtract #4
86939 atoms, 92348 bonds, 12 pseudobonds, 7918 residues, 2 models selected
> hide #!4 models
> hide #!2 models
> cartoon (#!3 & sel)
> select down
11 atoms, 11 bonds, 12 pseudobonds, 1 residue, 2 models selected
> select #3/l:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select ~sel
571071 atoms, 604546 bonds, 3397 pseudobonds, 53891 residues, 16 models
selected
> select subtract #1
483952 atoms, 512007 bonds, 3388 pseudobonds, 45944 residues, 14 models
selected
> select subtract #2
379716 atoms, 402037 bonds, 3358 pseudobonds, 35792 residues, 12 models
selected
> select subtract #4
275918 atoms, 292466 bonds, 1621 pseudobonds, 25713 residues, 8 models
selected
> select subtract #5
189014 atoms, 200152 bonds, 1610 pseudobonds, 17799 residues, 6 models
selected
> select subtract #6
85856 atoms, 91249 bonds, 9 pseudobonds, 7784 residues, 2 models selected
> cartoon hide (#!3 & sel)
> show #!2 models
> select clear
> show #!4 models
> hide #!3 models
> hide #!2 models
> select #4/l:161
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
128 atoms, 129 bonds, 16 residues, 1 model selected
> select up
526 atoms, 537 bonds, 66 residues, 1 model selected
> select up
546 atoms, 556 bonds, 68 residues, 1 model selected
> select up
872 atoms, 885 bonds, 107 residues, 1 model selected
> select ~sel
571282 atoms, 604760 bonds, 3396 pseudobonds, 53918 residues, 16 models
selected
> select subtract #3
484343 atoms, 512412 bonds, 3384 pseudobonds, 46000 residues, 14 models
selected
> select subtract #2
380107 atoms, 402442 bonds, 3354 pseudobonds, 35848 residues, 12 models
selected
> select subtract #1
292988 atoms, 309903 bonds, 3345 pseudobonds, 27901 residues, 10 models
selected
> select subtract #5
206084 atoms, 217589 bonds, 3334 pseudobonds, 19987 residues, 8 models
selected
> select subtract #6
102926 atoms, 108686 bonds, 1733 pseudobonds, 9972 residues, 4 models selected
> cartoon hide (#!4 & sel)
> hide #!4 models
> show #!5 models
> select add #4
103798 atoms, 109571 bonds, 1737 pseudobonds, 10079 residues, 4 models
selected
> select subtract #4
Nothing selected
> select #5/3:34
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> select add #5/i:28
548 atoms, 607 bonds, 27 residues, 1 model selected
> select up
1300 atoms, 1368 bonds, 121 residues, 1 model selected
> select add #5/l:161
1307 atoms, 1375 bonds, 122 residues, 1 model selected
> select up
2383 atoms, 2467 bonds, 255 residues, 1 model selected
> select ~sel
569771 atoms, 603178 bonds, 3397 pseudobonds, 53770 residues, 16 models
selected
> select subtract #4
465973 atoms, 493607 bonds, 1660 pseudobonds, 43691 residues, 12 models
selected
> select subtract #3
379034 atoms, 401259 bonds, 1648 pseudobonds, 35773 residues, 10 models
selected
> select subtract #2
274798 atoms, 291289 bonds, 1618 pseudobonds, 25621 residues, 8 models
selected
> select subtract #6
171640 atoms, 182386 bonds, 17 pseudobonds, 15606 residues, 4 models selected
> select subtract #1
84521 atoms, 89847 bonds, 8 pseudobonds, 7659 residues, 2 models selected
> surface (#!5 & sel)
> color #5 #ffaa00ff
> select clear
> select #5/i:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> color sel red
> select #5/l:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium orchid
> select clear
> select #5/3:18
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> color sel medium blue
> select clear
> transparency #5 10
> show #!3 models
> show #!2 models
> show #!4 models
> select #4/l:164
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
128 atoms, 129 bonds, 16 residues, 1 model selected
> select up
526 atoms, 537 bonds, 66 residues, 1 model selected
> select up
546 atoms, 556 bonds, 68 residues, 1 model selected
> select up
872 atoms, 885 bonds, 107 residues, 1 model selected
> select add #5/i:107
876 atoms, 888 bonds, 108 residues, 2 models selected
> select up
1780 atoms, 1803 bonds, 221 residues, 2 models selected
> select add #5/l:162
1787 atoms, 1810 bonds, 222 residues, 2 models selected
> select up
2863 atoms, 2902 bonds, 355 residues, 2 models selected
> view sel
> select clear
> lighting soft
> lighting simple
> lighting full
> lighting flat
> select #5/l:127
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel purple
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> save C:\ProgramData\ChimeraX\image78.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF2beta_intermediates.cxs"
> hide #!5 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!6 models
> view
> select #6/l:162
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
106 atoms, 109 bonds, 13 residues, 1 model selected
> select up
558 atoms, 571 bonds, 70 residues, 1 model selected
> select up
567 atoms, 579 bonds, 71 residues, 1 model selected
> select up
904 atoms, 919 bonds, 111 residues, 1 model selected
> select up
1048 atoms, 1064 bonds, 130 residues, 1 model selected
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/m:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
27 atoms, 26 bonds, 4 residues, 1 model selected
> select up
736 atoms, 744 bonds, 96 residues, 1 model selected
> show #!5 models
> hide #!6 models
> show #!2 models
> cartoon #2,5
> select #2/m:9
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
161 atoms, 167 bonds, 19 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> select ~sel
571014 atoms, 604481 bonds, 3400 pseudobonds, 53878 residues, 16 models
selected
> select subtract #1
483895 atoms, 511942 bonds, 3391 pseudobonds, 45931 residues, 52 models
selected
> select subtract #3
396956 atoms, 419594 bonds, 3379 pseudobonds, 38013 residues, 50 models
selected
> select subtract #4
293158 atoms, 310023 bonds, 1642 pseudobonds, 27934 residues, 46 models
selected
> select subtract #5
206254 atoms, 217709 bonds, 1631 pseudobonds, 20020 residues, 44 models
selected
> select subtract #6
103096 atoms, 108806 bonds, 30 pseudobonds, 10005 residues, 2 models selected
> cartoon hide (#!2 & sel)
> show #!4 models
> select add #2
104236 atoms, 109970 bonds, 30 pseudobonds, 10152 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #4
103798 atoms, 109571 bonds, 1737 pseudobonds, 10079 residues, 4 models
selected
> cartoon (#!4 & sel)
> select clear
> select #4/m:23
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
65 atoms, 66 bonds, 9 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> select ~sel
571438 atoms, 604921 bonds, 3400 pseudobonds, 53935 residues, 16 models
selected
> select subtract #1
484319 atoms, 512382 bonds, 3391 pseudobonds, 45988 residues, 52 models
selected
> select subtract #2
380083 atoms, 402412 bonds, 3361 pseudobonds, 35836 residues, 50 models
selected
> select subtract #3
293144 atoms, 310064 bonds, 3349 pseudobonds, 27918 residues, 48 models
selected
> select subtract #5
206240 atoms, 217750 bonds, 3338 pseudobonds, 20004 residues, 46 models
selected
> select subtract #6
103082 atoms, 108847 bonds, 1737 pseudobonds, 9989 residues, 4 models selected
> cartoon hide (#!4 & sel)
> save C:\ProgramData\ChimeraX\image79.png supersample 3
> save C:\ProgramData\ChimeraX\image80.png supersample 3
> hide #!5 models
> surface hidePatches (#!4 & sel)
> show #!5 models
> select add #5
189986 atoms, 201161 bonds, 1748 pseudobonds, 17903 residues, 6 models
selected
> select add #4
190702 atoms, 201885 bonds, 1748 pseudobonds, 17993 residues, 44 models
selected
> select subtract #4
86904 atoms, 92314 bonds, 11 pseudobonds, 7914 residues, 40 models selected
> surface hidePatches (#!5 & sel)
> show #!3 models
> hide #!5 models
> select subtract #5
38 models selected
> select add #3
86939 atoms, 92348 bonds, 12 pseudobonds, 7918 residues, 2 models selected
> cartoon (#!3 & sel)
> select clear
> select #3/l:184
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select ~sel
571071 atoms, 604546 bonds, 3397 pseudobonds, 53891 residues, 16 models
selected
> select subtract #2
466835 atoms, 494576 bonds, 3367 pseudobonds, 43739 residues, 52 models
selected
> select subtract #4
363037 atoms, 385005 bonds, 1630 pseudobonds, 33660 residues, 48 models
selected
> select subtract #5
276133 atoms, 292691 bonds, 1619 pseudobonds, 25746 residues, 46 models
selected
> select subtract #6
172975 atoms, 183788 bonds, 18 pseudobonds, 15731 residues, 4 models selected
> select subtract #1
85856 atoms, 91249 bonds, 9 pseudobonds, 7784 residues, 2 models selected
> surface (#!3 & sel)
> color #3 #ffaa00ff
> select clear
> select #3/l:144
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select up
86939 atoms, 92348 bonds, 7918 residues, 1 model selected
> select down
1083 atoms, 1099 bonds, 134 residues, 41 models selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orchid
> select clear
> select #3/l:160
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel purple
> select clear
> transparency #2-4 20
> select #3/i:110@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> color (#!3 & sel) red
> select clear
> select #4/m:106
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #4/m:107
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #4/m:105
22 atoms, 20 bonds, 3 residues, 1 model selected
> show sel target ab
> select #3/l:215
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
[Repeated 2 time(s)]
> cartoon hide sel
> select #3/l:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #3/l:201
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #3/l:197
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel atoms
> select #3/l:223
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> hide sel atoms
> select clear
> select #4/m:104
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
105 atoms, 106 bonds, 13 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> hide sel atoms
> select clear
> save C:\ProgramData\ChimeraX\image81.png supersample 3
> save C:\ProgramData\ChimeraX\image82.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF2beta_intermediates_2.cxs"
——— End of log from Sat May 6 17:06:28 2023 ———
opened ChimeraX session
> select #3/i:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> select add #2/m:102
805 atoms, 812 bonds, 100 residues, 3 models selected
> select up
869 atoms, 877 bonds, 109 residues, 3 models selected
> select up
1939 atoms, 1971 bonds, 246 residues, 3 models selected
> select add #4/m:48
1948 atoms, 1979 bonds, 247 residues, 4 models selected
> select up
2032 atoms, 2065 bonds, 257 residues, 4 models selected
> select up
2655 atoms, 2695 bonds, 336 residues, 4 models selected
> select add #3/l:179
2663 atoms, 2702 bonds, 337 residues, 4 models selected
> select up
3738 atoms, 3794 bonds, 470 residues, 4 models selected
> select ~sel & ##selected
291235 atoms, 308095 bonds, 1775 pseudobonds, 27679 residues, 8 models
selected
> hide sel cartoons
> select clear
> select #3/l:136
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark salmon
> color sel antique white
> color sel wheat
> color sel navajo white
> color sel pink
> color sel peach puff
> color sel navajo white
> color sel moccasin
> color sel bisque
> color sel misty rose
> color sel blanched almond
> color sel khaki
> color sel tan
> color sel burly wood
> color sel silver
> color sel light steel blue
> color sel green
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> show #!5 models
> hide #!5 models
> select #3/i:35
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> color (#!3 & sel) lime
> select clear
> select #2/m:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
46 atoms, 46 bonds, 6 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel red
> select clear
> select #4/m:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
93 atoms, 94 bonds, 11 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> color sel yellow
> select clear
> select #3/2:1248@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
33557 atoms, 37527 bonds, 1579 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark khaki
> color sel gold
> color sel dark khaki
> select clear
> select #3/f:87@C
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
584 atoms, 597 bonds, 74 residues, 2 models selected
> select up
585 atoms, 597 bonds, 75 residues, 2 models selected
> select up
86939 atoms, 92348 bonds, 7918 residues, 2 models selected
> color sel dark khaki
> undo
> select clear
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> select #3/2:1003@O2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
33557 atoms, 37527 bonds, 1579 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark khaki
> select #3/1:49@O3'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 22 bonds, 1 residue, 2 models selected
> select up
1639 atoms, 1828 bonds, 75 residues, 2 models selected
> select up
86939 atoms, 92348 bonds, 7918 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark khaki
> undo
> select clear
> select #3/f:85@CA
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
584 atoms, 597 bonds, 74 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark khaki
> select clear
> select #3/2:567@P
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 2 models selected
> select up
33557 atoms, 37527 bonds, 1579 residues, 2 models selected
> color sel dark khaki
[Repeated 1 time(s)]
> select #3/1:47@C5
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
1639 atoms, 1828 bonds, 75 residues, 2 models selected
> color sel dark khaki
> color sel beige
> color sel wheat
> select #3/2:995@OP2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
33557 atoms, 37527 bonds, 1579 residues, 2 models selected
> color sel beige
> color sel wheat
> select clear
> select #3/f:85@CB
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
584 atoms, 597 bonds, 74 residues, 2 models selected
> color sel wheat
> select #3/P:125@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
923 atoms, 942 bonds, 117 residues, 2 models selected
> color sel wheat
> select #3/S:144@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
1189 atoms, 1208 bonds, 145 residues, 2 models selected
> color sel wheat
> select #3/Z:28@C
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
594 atoms, 603 bonds, 78 residues, 2 models selected
> color sel wheat
> select #3/j:41@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
2145 atoms, 2177 bonds, 267 residues, 2 models selected
> color sel wheat
> select #3/F:209@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
1609 atoms, 1628 bonds, 206 residues, 2 models selected
> color sel wheat
> select clear
> select #3/B:54@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
1799 atoms, 1823 bonds, 225 residues, 2 models selected
> color sel wheat
> select clear
> select #3/k:256@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
3604 atoms, 3664 bonds, 471 residues, 2 models selected
> color sel wheat
> select #3/X:68@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
1119 atoms, 1137 bonds, 144 residues, 2 models selected
> color sel wheat
> select #3/h:23@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
233 atoms, 234 bonds, 25 residues, 2 models selected
> color sel wheat
> select #3/e:17@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
472 atoms, 480 bonds, 60 residues, 2 models selected
> color sel wheat
> select #3/D:178@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
1774 atoms, 1800 bonds, 227 residues, 2 models selected
> color sel wheat
> select #3/3:33@N3
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 2 models selected
> select up
536 atoms, 595 bonds, 26 residues, 2 models selected
> color sel wheat
> select #3/Q:143@CG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> color sel wheat
> select clear
> select #3/C:40@N
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> color sel wheat
> select clear
> select #3/C:37@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
1648 atoms, 1678 bonds, 220 residues, 2 models selected
> color sel wheat
> select clear
> select #3/Q:142@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> color sel wheat
> select clear
> show #!2 models
> show #!4 models
> select #4/m:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
105 atoms, 106 bonds, 13 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> color sel cyan
> select clear
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> save C:\ProgramData\ChimeraX\image139.png supersample 3
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #3/l:162
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> hide sel cartoons
> select #3/1:36@O3'
1 atom, 1 residue, 1 model selected
> select #3/i:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> hide sel cartoons
> show #!5 models
> select #5/i:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> color sel lime
> select clear
> select #5/i:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> select add #5/l:157
773 atoms, 781 bonds, 96 residues, 1 model selected
> select up
1847 atoms, 1872 bonds, 229 residues, 1 model selected
> select ~sel & ##selected
85057 atoms, 90442 bonds, 8 pseudobonds, 7685 residues, 2 models selected
> hide sel cartoons
> select clear
> select #5/l:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark green
> color sel green
> select clear
> select #5/l:181
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel forest green
> ui tool show "Color Actions"
> color sel dark green
> select clear
> select #5/l:241
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel green
> select clear
> select #3/k:255@NE
1 atom, 1 residue, 1 model selected
> select add #3/k:255@NH2
2 atoms, 1 residue, 2 models selected
> select add #3/k:255@CD
3 atoms, 1 residue, 2 models selected
> select add #3/k:255@NH1
4 atoms, 1 residue, 2 models selected
> select add #3/k:255@CG
5 atoms, 1 residue, 2 models selected
> select add #3/k:256@N
6 atoms, 2 residues, 2 models selected
> select add #3/k:255@CA
7 atoms, 2 residues, 2 models selected
> select add #3/k:255@CB
8 atoms, 2 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select #3/k:255@CZ
1 atom, 1 residue, 1 model selected
> select add #3/k:256@OE1
2 atoms, 2 residues, 2 models selected
> select add #3/k:256@CB
3 atoms, 2 residues, 2 models selected
> select add #3/k:256@CG
4 atoms, 2 residues, 2 models selected
> select add #3/k:256@CD
5 atoms, 2 residues, 2 models selected
> select add #3/k:256@OE2
6 atoms, 2 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select #3/k:257@N
1 atom, 1 residue, 1 model selected
> select add #3/k:257@CB
2 atoms, 1 residue, 2 models selected
> select subtract #3/k:257@CB
1 atom, 1 residue, 2 models selected
Drag select of beta_no1_cl2_rsr_real_space_refined.cif_k SES surface, 226 of
438680 triangles, 1 residues
> select #3/k:257@N
1 atom, 1 residue, 1 model selected
> select add #3/k:257@CB
2 atoms, 1 residue, 2 models selected
> select add #3/k:256@O
3 atoms, 2 residues, 2 models selected
> select add #3/k:256@C
4 atoms, 2 residues, 2 models selected
> select add #3/k:257@CG
5 atoms, 2 residues, 2 models selected
> select add #3/k:257@CA
6 atoms, 2 residues, 2 models selected
> select add #3/k:257@OE2
7 atoms, 2 residues, 2 models selected
> select add #3/k:257@CD
8 atoms, 2 residues, 2 models selected
> select add #3/k:257@OE1
9 atoms, 2 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select #3/k:261@CG
1 atom, 1 residue, 1 model selected
> select #3/k:257@O
1 atom, 1 residue, 1 model selected
> select add #3/k:260@CB
2 atoms, 2 residues, 2 models selected
> select add #3/k:261@N
3 atoms, 3 residues, 2 models selected
> select add #3/k:261@CG
4 atoms, 3 residues, 2 models selected
> select add #3/k:261@CA
5 atoms, 3 residues, 2 models selected
> select add #3/k:261@CD
6 atoms, 3 residues, 2 models selected
> select add #3/k:261@OE2
7 atoms, 3 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select clear
> save C:\ProgramData\ChimeraX\image140.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF2beta_eIF1A_eIF5placement.cxs"
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> save C:\ProgramData\ChimeraX\image141.png supersample 3
> hide #!5 models
> hide #!3 models
> show #!3 models
> select #3/I
1489 atoms, 1515 bonds, 1 pseudobond, 188 residues, 2 models selected
> show sel cartoons
> select #4/m#6/m
1452 atoms, 1468 bonds, 186 residues, 2 models selected
> show sel & #!4 cartoons
> select clear
> close #6
> show #!1 models
> hide #!1 models
> close #1
> select #2/I#3/I#5/I
4467 atoms, 4545 bonds, 3 pseudobonds, 564 residues, 6 models selected
> show sel & #!2-3 cartoons
> select #3/l
1083 atoms, 1099 bonds, 3 pseudobonds, 134 residues, 2 models selected
> show sel cartoons
> select clear
> select #4/i
884 atoms, 894 bonds, 111 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select clear
> select #3/i
799 atoms, 807 bonds, 1 pseudobond, 99 residues, 2 models selected
> show sel cartoons
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save C:\ProgramData\ChimeraX\image142.png supersample 3
> save C:\ProgramData\ChimeraX\image143.png supersample 3
> select #3/l:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel purple
> select clear
[Repeated 1 time(s)]
> select #3/l:144
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel blue
> select clear
> select #2/m:12
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
161 atoms, 167 bonds, 19 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel magenta
> color sel hot pink
> select clear
> select #4/m:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
105 atoms, 106 bonds, 13 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> color sel coral
> color sel brown
> color sel tomato
> color sel dark khaki
> color sel medium turquoise
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel peru
> color sel dark goldenrod
> color sel gold
> select clear
> select #4/m:35
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
59 atoms, 58 bonds, 7 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> select clear
> select #3/i:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> ui tool show "Color Actions"
> color sel spring green
> color sel lawn green
> select clear
> select #4/m:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
105 atoms, 106 bonds, 13 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> color sel red
> select #2/m:13
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
161 atoms, 167 bonds, 19 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel yellow
> ui tool show "Color Actions"
> color sel gold
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel dark orange
> select clear
> select #2/m:124
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 2 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel yellow
> select clear
> select #2/m:12
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
161 atoms, 167 bonds, 19 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep pink
> color sel blue violet
> color sel medium orchid
> color sel dark orchid
> color sel purple
> color sel dark orchid
> color sel medium orchid
> color sel orchid
> color sel hot pink
> color sel blue violet
> color sel dark violet
> color sel dark orchid
> color sel medium orchid
> color sel pale violet red
> color sel medium purple
> color sel medium orchid
> color sel blue violet
> color sel black
> color sel pale green
> color sel light green
> color sel dark sea green
> color sel pale turquoise
> color sel powder blue
> color sel sky blue
> color sel magenta
> color sel sky blue
> color sel light sky blue
> color sel powder blue
> color sel pale turquoise
> color sel light cyan
> color sel sky blue
> color sel light sky blue
> color sel pale turquoise
> color sel light sky blue
> select clear
> select #3/l:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel yellow
> select clear
> select #3/l:143
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light yellow
> color sel white
> color sel white smoke
> color sel light pink
> color sel deep sky blue
> color sel navy
> color sel royal blue
> color sel deep sky blue
> color sel cyan
> color sel deep sky blue
> select clear
> select #2/m:11
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
161 atoms, 167 bonds, 19 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel blue
> color sel medium blue
> color sel dark blue
> color sel navy
> color sel indigo
> color sel royal blue
> color sel medium violet red
> color sel gold
> color sel yellow
> select clear
> select #3/i:110
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> ui tool show "Color Actions"
> color sel olive
> color sel lime
> color sel green
> color sel chartreuse
> color sel lawn green
> color sel lime green
> color sel forest green
> select clear
> select #3/i:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> color (#!3 & sel) orange
> select clear
> select #2/m:13
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
161 atoms, 167 bonds, 19 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel lime
> select clear
> save C:\ProgramData\ChimeraX\image144.png supersample 3
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/l:144
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> hide #!3 models
> show #!3 models
> select #5/i:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> color sel orange
> select clear
> select #3/i:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
799 atoms, 807 bonds, 99 residues, 2 models selected
> hide sel cartoons
> hide #!5 models
> show #!5 models
> select #3/l:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select up
86939 atoms, 92348 bonds, 7918 residues, 1 model selected
> select down
1083 atoms, 1099 bonds, 134 residues, 41 models selected
> hide sel cartoons
> save C:\ProgramData\ChimeraX\image145.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/eIF2beta_eIF1A_eIF5placement.cxs"
——— End of log from Mon Aug 28 16:12:33 2023 ———
opened ChimeraX session
> hide #!3 models
> show #!3 models
> select #5/i:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> select #2/m:101
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
70 atoms, 70 bonds, 10 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel cyan
> select clear
> select #5/l:144
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #4/m:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
73 atoms, 73 bonds, 9 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> color sel cyan
> select clear
> select #2/m:124
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 2 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel #000099ff
> color sel #009966ff
> select clear
> select #5/l:143
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel red
> select clear
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> close session
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/beta_no1_cl3_rsr_real_space_refined.pdb"
Chain information for beta_no1_cl3_rsr_real_space_refined.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/beta_no1_cl2_rsr_real_space_refined
> 1.pdb"
Chain information for beta_no1_cl2_rsr_real_space_refined 1.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> show cartoons
> hide atoms
> set bgColor white
> graphics silhouettes true
> lighting soft
> lighting shadows true intensity 0.5
> select #1/A#2/A
3404 atoms, 3484 bonds, 438 residues, 2 models selected
> color sel #000099ff
> color sel #ffffffff
> color sel #ffffa7ff
> select #1/B#2/B
3598 atoms, 3644 bonds, 4 pseudobonds, 450 residues, 4 models selected
> select #1/C#2/C
3296 atoms, 3356 bonds, 440 residues, 2 models selected
> select #1/E#2/E
4156 atoms, 4244 bonds, 520 residues, 2 models selected
> select #1/F#2/F
3218 atoms, 3256 bonds, 412 residues, 2 models selected
> select #1/G#2/G
3664 atoms, 3710 bonds, 460 residues, 2 models selected
> select #1/H#2/H
2966 atoms, 3014 bonds, 368 residues, 2 models selected
> select #1/I#2/I
2978 atoms, 3030 bonds, 2 pseudobonds, 376 residues, 4 models selected
> select #1/J#2/J
2942 atoms, 2990 bonds, 364 residues, 2 models selected
> select #1/L#2/L
2496 atoms, 2552 bonds, 310 residues, 2 models selected
> select #1/N#2/N
2390 atoms, 2436 bonds, 302 residues, 2 models selected
> select #1/O#2/O
1910 atoms, 1932 bonds, 258 residues, 2 models selected
> select #1/H#2/H
2966 atoms, 3014 bonds, 368 residues, 2 models selected
> select #1/I#2/I
2978 atoms, 3030 bonds, 2 pseudobonds, 376 residues, 4 models selected
> select #1/J#2/J
2942 atoms, 2990 bonds, 364 residues, 2 models selected
> select #1/L#2/L
2496 atoms, 2552 bonds, 310 residues, 2 models selected
> select #1/N#2/N
2390 atoms, 2436 bonds, 302 residues, 2 models selected
> select #1/O#2/O
1910 atoms, 1932 bonds, 258 residues, 2 models selected
> select #1/V#2/V
1374 atoms, 1392 bonds, 174 residues, 2 models selected
> select #1/W#2/W
2042 atoms, 2078 bonds, 258 residues, 2 models selected
> select #1/X#2/X
2238 atoms, 2274 bonds, 288 residues, 2 models selected
> select #1/Y#2/Y
2122 atoms, 2150 bonds, 268 residues, 2 models selected
> select #1/a#2/a
1596 atoms, 1620 bonds, 206 residues, 2 models selected
> select #1/b#2/b
1220 atoms, 1238 bonds, 164 residues, 2 models selected
> select #1/e#2/e
944 atoms, 960 bonds, 120 residues, 2 models selected
> select #1/h#2/h
466 atoms, 468 bonds, 50 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/2 #2/2
Alignment identifier is 1
> select #1/2:1 #2/2:1
40 atoms, 42 bonds, 2 residues, 2 models selected
> select #1/2:1-1149 #2/2:1-1149
48940 atoms, 54742 bonds, 2298 residues, 2 models selected
1 [ID: 1] region 2 chains [1-1149] RMSD: 0.852
> ui tool show "Color Actions"
> color sel #ffffffff
> color sel #ffffa7ff
> select #1/2:1626-1627 #2/2:1626-1627
86 atoms, 94 bonds, 4 residues, 2 models selected
> select #1/2:1626-1798 #2/2:1626-1798
7134 atoms, 7970 bonds, 346 residues, 2 models selected
1 [ID: 1] region 2 chains [1626-1798] RMSD: 0.951
> color sel #ffffffff
> color sel #ffffa7ff
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/X:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
52 atoms, 53 bonds, 6 residues, 1 model selected
> select up
1119 atoms, 1137 bonds, 144 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> show #!2 models
> hide #!1 models
> select #2/X:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 13 residues, 1 model selected
> select up
1119 atoms, 1137 bonds, 144 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #2/V:51
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
51 atoms, 52 bonds, 6 residues, 1 model selected
> select up
687 atoms, 696 bonds, 87 residues, 1 model selected
> select add #2/C:75
695 atoms, 703 bonds, 88 residues, 1 model selected
> select up
748 atoms, 757 bonds, 94 residues, 1 model selected
> select up
2335 atoms, 2374 bonds, 307 residues, 1 model selected
> select add #2/J:128
2343 atoms, 2381 bonds, 308 residues, 1 model selected
> select up
2400 atoms, 2440 bonds, 315 residues, 1 model selected
> select up
3806 atoms, 3869 bonds, 489 residues, 1 model selected
> select add #2/H:183
3817 atoms, 3880 bonds, 490 residues, 1 model selected
> select up
3849 atoms, 3912 bonds, 494 residues, 1 model selected
> select up
5289 atoms, 5376 bonds, 673 residues, 1 model selected
> select add #2/Y:72
5300 atoms, 5387 bonds, 674 residues, 1 model selected
> select up
5357 atoms, 5445 bonds, 682 residues, 1 model selected
> select up
6350 atoms, 6451 bonds, 807 residues, 1 model selected
> select add #2/G:207
6359 atoms, 6459 bonds, 808 residues, 1 model selected
> select up
6741 atoms, 6843 bonds, 856 residues, 1 model selected
> select up
8182 atoms, 8306 bonds, 1037 residues, 1 model selected
> select add #2/I:92
8193 atoms, 8316 bonds, 1038 residues, 1 model selected
> select up
8232 atoms, 8355 bonds, 1043 residues, 1 model selected
> select up
9157 atoms, 9299 bonds, 1159 residues, 1 model selected
> select up
9170 atoms, 9311 bonds, 1161 residues, 1 model selected
> select add #2/I:197
9178 atoms, 9318 bonds, 1162 residues, 1 model selected
> select up
9287 atoms, 9429 bonds, 1175 residues, 1 model selected
> select up
9671 atoms, 9821 bonds, 1225 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #2/h:22
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
205 atoms, 206 bonds, 22 residues, 1 model selected
> select add #2/N:119
214 atoms, 214 bonds, 23 residues, 1 model selected
> select up
418 atoms, 422 bonds, 46 residues, 1 model selected
> select up
1428 atoms, 1452 bonds, 176 residues, 1 model selected
> select add #2/W:62
1435 atoms, 1458 bonds, 177 residues, 1 model selected
> select up
1459 atoms, 1482 bonds, 180 residues, 1 model selected
> select up
2449 atoms, 2491 bonds, 305 residues, 1 model selected
> select add #2/L:105
2458 atoms, 2499 bonds, 306 residues, 1 model selected
> select up
2557 atoms, 2602 bonds, 317 residues, 1 model selected
> select up
3697 atoms, 3767 bonds, 460 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #2/b:80
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
39 atoms, 39 bonds, 4 residues, 1 model selected
> select up
609 atoms, 619 bonds, 81 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #2/l:227
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
123 atoms, 123 bonds, 14 residues, 1 model selected
> select up
346 atoms, 348 bonds, 41 residues, 1 model selected
> select up
494 atoms, 496 bonds, 61 residues, 1 model selected
> select up
893 atoms, 905 bonds, 111 residues, 1 model selected
> select up
925 atoms, 937 bonds, 115 residues, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel red
> select #2/k:264
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
116 atoms, 117 bonds, 14 residues, 1 model selected
> select up
3596 atoms, 3657 bonds, 470 residues, 1 model selected
> color sel orange
> select clear
> select #2/1:67
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1827 bonds, 75 residues, 1 model selected
> select up
86939 atoms, 92347 bonds, 7918 residues, 1 model selected
> select down
1639 atoms, 1827 bonds, 75 residues, 1 model selected
> color sel cyan
> color sel forest green
> select #2/j:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
120 atoms, 120 bonds, 14 residues, 1 model selected
> select up
1462 atoms, 1488 bonds, 177 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #2/i:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
764 atoms, 773 bonds, 95 residues, 1 model selected
> color sel #5555ffff
> select clear
> select #2/3:30
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
536 atoms, 595 bonds, 26 residues, 1 model selected
> color sel #ff00ffff
> select clear
> show #!1 models
> hide #!2 models
> select #1/J:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
1471 atoms, 1495 bonds, 182 residues, 1 model selected
> select add #1/Y:46
1480 atoms, 1503 bonds, 183 residues, 1 model selected
> select up
1561 atoms, 1584 bonds, 193 residues, 1 model selected
> select up
2532 atoms, 2570 bonds, 316 residues, 1 model selected
> select add #1/H:32
2539 atoms, 2577 bonds, 317 residues, 1 model selected
> select up
2562 atoms, 2600 bonds, 320 residues, 1 model selected
> select up
4015 atoms, 4077 bonds, 500 residues, 1 model selected
> select add #1/N:32
4019 atoms, 4080 bonds, 501 residues, 1 model selected
> select up
4127 atoms, 4189 bonds, 514 residues, 1 model selected
> select up
5210 atoms, 5295 bonds, 651 residues, 1 model selected
> select add #1/I:191
5215 atoms, 5299 bonds, 652 residues, 1 model selected
> select up
5327 atoms, 5413 bonds, 665 residues, 1 model selected
> select up
5724 atoms, 5817 bonds, 717 residues, 1 model selected
> select up
5772 atoms, 5865 bonds, 724 residues, 1 model selected
> select up
6699 atoms, 6810 bonds, 839 residues, 1 model selected
> select add #1/G:191
6708 atoms, 6818 bonds, 840 residues, 1 model selected
> select up
7090 atoms, 7202 bonds, 888 residues, 1 model selected
> select up
8531 atoms, 8665 bonds, 1069 residues, 1 model selected
> select subtract #1/Y:46
8522 atoms, 8655 bonds, 1068 residues, 1 model selected
> select up
8531 atoms, 8665 bonds, 1069 residues, 1 model selected
> select up
86904 atoms, 92313 bonds, 7914 residues, 1 model selected
> select down
8531 atoms, 8665 bonds, 1069 residues, 1 model selected
> color sel #ffff00ff
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #1/h:23
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
205 atoms, 206 bonds, 22 residues, 1 model selected
> select add #1/L:76
212 atoms, 212 bonds, 23 residues, 1 model selected
> select up
259 atoms, 259 bonds, 30 residues, 1 model selected
> select up
1481 atoms, 1510 bonds, 180 residues, 1 model selected
> select add #1/W:42
1490 atoms, 1518 bonds, 181 residues, 1 model selected
> select up
1593 atoms, 1623 bonds, 193 residues, 1 model selected
> select up
2502 atoms, 2549 bonds, 309 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #1/b:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
40 atoms, 40 bonds, 5 residues, 1 model selected
> select up
609 atoms, 619 bonds, 81 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #1/V:73
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 12 residues, 1 model selected
> select up
687 atoms, 696 bonds, 87 residues, 1 model selected
> select add #1/C:76
696 atoms, 704 bonds, 88 residues, 1 model selected
> select up
748 atoms, 757 bonds, 94 residues, 1 model selected
> select up
2335 atoms, 2374 bonds, 307 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> select #1/M:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 11 residues, 1 model selected
> select up
430 atoms, 430 bonds, 58 residues, 1 model selected
> select up
497 atoms, 497 bonds, 67 residues, 1 model selected
> select up
885 atoms, 891 bonds, 117 residues, 1 model selected
> select add #1/U:45
890 atoms, 895 bonds, 118 residues, 1 model selected
> select up
1008 atoms, 1013 bonds, 133 residues, 1 model selected
> select up
1730 atoms, 1748 bonds, 223 residues, 1 model selected
> select add #1/P:41
1737 atoms, 1754 bonds, 224 residues, 1 model selected
> select up
1800 atoms, 1818 bonds, 231 residues, 1 model selected
> select up
2653 atoms, 2690 bonds, 340 residues, 1 model selected
> select add #1/F:217
2661 atoms, 2697 bonds, 341 residues, 1 model selected
> select up
2777 atoms, 2814 bonds, 355 residues, 1 model selected
> select up
4262 atoms, 4318 bonds, 546 residues, 1 model selected
> select add #1/c:42
4273 atoms, 4328 bonds, 547 residues, 1 model selected
> select up
4319 atoms, 4374 bonds, 553 residues, 1 model selected
> select up
4761 atoms, 4819 bonds, 610 residues, 1 model selected
> select up
86904 atoms, 92313 bonds, 7914 residues, 1 model selected
> select down
4761 atoms, 4819 bonds, 610 residues, 1 model selected
> select add #1/g:9
4768 atoms, 4825 bonds, 611 residues, 1 model selected
> select up
4822 atoms, 4879 bonds, 618 residues, 1 model selected
> select up
5999 atoms, 6081 bonds, 772 residues, 1 model selected
> select up
6037 atoms, 6118 bonds, 777 residues, 1 model selected
> select up
6178 atoms, 6262 bonds, 795 residues, 1 model selected
> select up
6291 atoms, 6377 bonds, 809 residues, 1 model selected
> select up
7230 atoms, 7342 bonds, 930 residues, 1 model selected
> select up
86904 atoms, 92313 bonds, 7914 residues, 1 model selected
> select down
7230 atoms, 7342 bonds, 930 residues, 1 model selected
> select add #1/R:21
7242 atoms, 7354 bonds, 931 residues, 1 model selected
> select up
7372 atoms, 7486 bonds, 947 residues, 1 model selected
> select up
8263 atoms, 8386 bonds, 1060 residues, 1 model selected
> select add #1/Q:104
8272 atoms, 8394 bonds, 1061 residues, 1 model selected
> select up
8353 atoms, 8476 bonds, 1071 residues, 1 model selected
> select up
9368 atoms, 9511 bonds, 1201 residues, 1 model selected
> color sel #ffffffff
> color sel #ff88ddff
> color sel #f8d568ff
> select clear
> select #1/f:137
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
34 atoms, 35 bonds, 3 residues, 1 model selected
> select up
584 atoms, 597 bonds, 74 residues, 1 model selected
> select add #1/D:71
592 atoms, 604 bonds, 75 residues, 1 model selected
> select up
731 atoms, 744 bonds, 91 residues, 1 model selected
> select up
2358 atoms, 2397 bonds, 301 residues, 1 model selected
> select add #1/T:106
2367 atoms, 2405 bonds, 302 residues, 1 model selected
> select up
2464 atoms, 2502 bonds, 314 residues, 1 model selected
> select up
3468 atoms, 3526 bonds, 444 residues, 1 model selected
> select add #1/S:77
3475 atoms, 3532 bonds, 445 residues, 1 model selected
> select up
3504 atoms, 3564 bonds, 448 residues, 1 model selected
> select up
4657 atoms, 4734 bonds, 589 residues, 1 model selected
> select up
4658 atoms, 4734 bonds, 590 residues, 1 model selected
> select add #1/Z:102
4665 atoms, 4740 bonds, 591 residues, 1 model selected
> select up
4696 atoms, 4772 bonds, 594 residues, 1 model selected
> select up
5252 atoms, 5337 bonds, 668 residues, 1 model selected
> color sel #ff88ddff
> color sel #f8d568ff
> select clear
> select #1/K:78
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
88 atoms, 89 bonds, 10 residues, 1 model selected
> select up
809 atoms, 831 bonds, 96 residues, 1 model selected
> lighting shadows false
> color sel #ff88ddff
> color sel #f8d568ff
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/2 #2/2
Alignment identifier is 1
> select #1/2:1150 #2/2:1150
44 atoms, 48 bonds, 2 residues, 2 models selected
> select #1/2:1150-1625 #2/2:1150-1625
20306 atoms, 22695 bonds, 1 pseudobond, 952 residues, 3 models selected
1 [ID: 1] region 2 chains [1150-1625] RMSD: 0.687
> color (#!1 & sel) #ff88ddff
> color (#!1 & sel) #f8d568ff
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/2 #2/2
Alignment identifier is 1
> select #1/2:1150 #2/2:1150
44 atoms, 48 bonds, 2 residues, 2 models selected
> select #1/2:1150-1625 #2/2:1150-1625
20306 atoms, 22695 bonds, 1 pseudobond, 952 residues, 3 models selected
1 [ID: 1] region 2 chains [1150-1625] RMSD: 0.687
> color (#!2 & sel) #ff88ddff
> color (#!2 & sel) #f8d568ff
> select clear
> select #2/S:115
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
150 atoms, 149 bonds, 18 residues, 1 model selected
> select up
1189 atoms, 1208 bonds, 145 residues, 1 model selected
> select add #2/P:65
1197 atoms, 1215 bonds, 146 residues, 1 model selected
> select up
1300 atoms, 1319 bonds, 160 residues, 1 model selected
> select up
2112 atoms, 2150 bonds, 262 residues, 1 model selected
> select add #2/M:66
2121 atoms, 2158 bonds, 263 residues, 1 model selected
> select up
2188 atoms, 2225 bonds, 273 residues, 1 model selected
> select up
2542 atoms, 2580 bonds, 320 residues, 1 model selected
> select up
2609 atoms, 2647 bonds, 329 residues, 1 model selected
> select up
2997 atoms, 3041 bonds, 379 residues, 1 model selected
> select add #2/K:17
3006 atoms, 3049 bonds, 380 residues, 1 model selected
> select up
3128 atoms, 3174 bonds, 393 residues, 1 model selected
> select up
3806 atoms, 3872 bonds, 475 residues, 1 model selected
> select up
86939 atoms, 92347 bonds, 7918 residues, 1 model selected
> select down
3806 atoms, 3872 bonds, 475 residues, 1 model selected
> select add #2/D:71
3814 atoms, 3879 bonds, 476 residues, 1 model selected
> select up
3953 atoms, 4019 bonds, 492 residues, 1 model selected
> select up
5580 atoms, 5672 bonds, 702 residues, 1 model selected
> select add #2/T:110
5589 atoms, 5680 bonds, 703 residues, 1 model selected
> select up
5690 atoms, 5781 bonds, 716 residues, 1 model selected
> select up
6690 atoms, 6801 bonds, 845 residues, 1 model selected
> select add #2/Z:51
6698 atoms, 6808 bonds, 846 residues, 1 model selected
> select up
6780 atoms, 6891 bonds, 855 residues, 1 model selected
> select up
7284 atoms, 7404 bonds, 923 residues, 1 model selected
> select add #2/j:109
7294 atoms, 7414 bonds, 924 residues, 1 model selected
> select up
7504 atoms, 7627 bonds, 949 residues, 1 model selected
> select up
8746 atoms, 8892 bonds, 1100 residues, 1 model selected
> color sel #ff88ddff
> color sel #f8d568ff
> select clear
> select #2/U:102
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
74 atoms, 74 bonds, 9 residues, 1 model selected
> select up
845 atoms, 857 bonds, 106 residues, 1 model selected
> select add #2/g:175
852 atoms, 863 bonds, 107 residues, 1 model selected
> select up
889 atoms, 901 bonds, 112 residues, 1 model selected
> select up
1024 atoms, 1038 bonds, 129 residues, 1 model selected
> select up
1184 atoms, 1200 bonds, 150 residues, 1 model selected
> select up
3314 atoms, 3380 bonds, 426 residues, 1 model selected
> select up
86939 atoms, 92347 bonds, 7918 residues, 1 model selected
> select down
3314 atoms, 3380 bonds, 426 residues, 1 model selected
> select add #2/R:19
3323 atoms, 3388 bonds, 427 residues, 1 model selected
> select up
3456 atoms, 3524 bonds, 443 residues, 1 model selected
> select up
4347 atoms, 4424 bonds, 556 residues, 1 model selected
> select add #2/Q:68
4356 atoms, 4432 bonds, 557 residues, 1 model selected
> select up
4412 atoms, 4488 bonds, 564 residues, 1 model selected
> select up
5452 atoms, 5549 bonds, 697 residues, 1 model selected
> select add #2/F:137
5460 atoms, 5556 bonds, 698 residues, 1 model selected
> select up
5540 atoms, 5637 bonds, 709 residues, 1 model selected
> select up
7061 atoms, 7177 bonds, 903 residues, 1 model selected
> color sel #ff88ddff
> color sel #f8d568ff
> select clear
> select #2/f:104
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
35 atoms, 35 bonds, 4 residues, 1 model selected
> select up
584 atoms, 597 bonds, 74 residues, 1 model selected
> color sel #ff88ddff
> color sel #f8d568ff
> select clear
> show #!1 models
> select #1/1#2/1
3278 atoms, 3654 bonds, 6 pseudobonds, 150 residues, 4 models selected
> color (#!1-2 & sel) #ff88ddff
> color (#!1-2 & sel) #000066ff
> color (#!1-2 & sel) #006f46ff
> select #1/j#2/j
4290 atoms, 4354 bonds, 2 pseudobonds, 534 residues, 4 models selected
> color (#!1-2 & sel) #000066ff
> color (#!1-2 & sel) #886666ff
> color (#!1-2 & sel) #8661a5ff
> select #1/i#2/i
1563 atoms, 1580 bonds, 1 pseudobond, 194 residues, 3 models selected
> color (#!1-2 & sel) #886666ff
> color (#!1-2 & sel) #441144ff
> color (#!1-2 & sel) #4147c0ff
> select #1/3#2/3
1072 atoms, 1190 bonds, 52 residues, 2 models selected
> color sel #441144ff
> color sel #dd7744ff
> color sel #d7459dff
> select #1/k#2/k
7274 atoms, 7396 bonds, 2 pseudobonds, 946 residues, 4 models selected
> color (#!1-2 & sel) #dd7744ff
> color (#!1-2 & sel) #ff8899ff
> color (#!1-2 & sel) #f8973cff
> select clear
> select #1/l:231
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
123 atoms, 123 bonds, 14 residues, 1 model selected
> select up
346 atoms, 348 bonds, 41 residues, 1 model selected
> select up
494 atoms, 496 bonds, 61 residues, 1 model selected
> select up
893 atoms, 905 bonds, 111 residues, 1 model selected
> select up
925 atoms, 937 bonds, 115 residues, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> color sel red
> select clear
> hide #!1 models
> select #2/O:73
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
129 atoms, 130 bonds, 18 residues, 1 model selected
> select up
955 atoms, 966 bonds, 129 residues, 1 model selected
> select add #2/B:229
963 atoms, 973 bonds, 130 residues, 1 model selected
> select up
1003 atoms, 1013 bonds, 136 residues, 1 model selected
> select up
2690 atoms, 2726 bonds, 345 residues, 1 model selected
> color sel #ff8899ff
> color sel #ffffffff
> color sel #ffffa7ff
> show #!1 models
> hide #!2 models
> select #1/O:73
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
129 atoms, 130 bonds, 18 residues, 1 model selected
> select up
955 atoms, 966 bonds, 129 residues, 1 model selected
> select add #1/B:229
963 atoms, 973 bonds, 130 residues, 1 model selected
> select up
1003 atoms, 1013 bonds, 136 residues, 1 model selected
> select up
2690 atoms, 2726 bonds, 345 residues, 1 model selected
> select add #1/a:51
2701 atoms, 2736 bonds, 346 residues, 1 model selected
> select up
2819 atoms, 2852 bonds, 363 residues, 1 model selected
> select up
3551 atoms, 3598 bonds, 456 residues, 1 model selected
> color sel #ffffffff
> color sel #ffffa7ff
> select clear
> ribbon style width 1 thickness 1
> cartoon style width 1 thickness 1
[Repeated 1 time(s)]
> undo
[Repeated 2 time(s)]
> select #1/1:10
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1827 bonds, 75 residues, 1 model selected
> select add #1/j:171
1647 atoms, 1834 bonds, 76 residues, 1 model selected
> select up
1759 atoms, 1947 bonds, 89 residues, 1 model selected
> select up
3101 atoms, 3315 bonds, 252 residues, 1 model selected
> select up
3106 atoms, 3319 bonds, 253 residues, 1 model selected
> select up
3784 atoms, 4004 bonds, 342 residues, 1 model selected
> select add #1/k:64
3793 atoms, 4012 bonds, 343 residues, 1 model selected
> select up
3889 atoms, 4109 bonds, 353 residues, 1 model selected
> select up
7380 atoms, 7661 bonds, 812 residues, 1 model selected
> select up
7388 atoms, 7668 bonds, 813 residues, 1 model selected
> select up
7421 atoms, 7702 bonds, 815 residues, 1 model selected
> select up
86904 atoms, 92313 bonds, 7914 residues, 1 model selected
> select down
7421 atoms, 7702 bonds, 815 residues, 1 model selected
> select add #1/l:140
7429 atoms, 7709 bonds, 816 residues, 1 model selected
> select up
7541 atoms, 7823 bonds, 829 residues, 1 model selected
> select up
7611 atoms, 7896 bonds, 838 residues, 1 model selected
> select up
7684 atoms, 7972 bonds, 847 residues, 1 model selected
> select up
8014 atoms, 8308 bonds, 889 residues, 1 model selected
> select up
8023 atoms, 8316 bonds, 890 residues, 1 model selected
> select up
8360 atoms, 8656 bonds, 930 residues, 1 model selected
> select up
8504 atoms, 8801 bonds, 949 residues, 1 model selected
> select subtract #1/1:47
8484 atoms, 8778 bonds, 948 residues, 1 model selected
> select up
8504 atoms, 8801 bonds, 949 residues, 1 model selected
> surface sel
> select clear
> undo
> surface hidePatches (#!1 & sel)
> select ~sel & ##selected
78400 atoms, 83512 bonds, 6 pseudobonds, 6965 residues, 2 models selected
> surface (#!1 & sel)
> select clear
> show #!2 models
> hide #!1 models
> select #2/l:227
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
123 atoms, 123 bonds, 14 residues, 1 model selected
> select up
346 atoms, 348 bonds, 41 residues, 1 model selected
> select up
494 atoms, 496 bonds, 61 residues, 1 model selected
> select up
893 atoms, 905 bonds, 111 residues, 1 model selected
> select up
925 atoms, 937 bonds, 115 residues, 1 model selected
> select up
1083 atoms, 1099 bonds, 134 residues, 1 model selected
> select add #2/k:260
1091 atoms, 1106 bonds, 135 residues, 1 model selected
> select up
1199 atoms, 1216 bonds, 148 residues, 1 model selected
> select up
4679 atoms, 4756 bonds, 604 residues, 1 model selected
> select add #2/j:209
4688 atoms, 4764 bonds, 605 residues, 1 model selected
> select up
4791 atoms, 4866 bonds, 619 residues, 1 model selected
> select up
5370 atoms, 5452 bonds, 695 residues, 1 model selected
> select up
5392 atoms, 5474 bonds, 698 residues, 1 model selected
> select up
6832 atoms, 6940 bonds, 872 residues, 1 model selected
> select add #2/1:66
6852 atoms, 6961 bonds, 873 residues, 1 model selected
> select up
8471 atoms, 8767 bonds, 947 residues, 1 model selected
> select up
8504 atoms, 8802 bonds, 949 residues, 1 model selected
> select ~sel & ##selected
78435 atoms, 83545 bonds, 8 pseudobonds, 6969 residues, 2 models selected
> surface (#!2 & sel)
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/new_session_files/2beta_TC_conformations_new.cxs"
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> select #2/1:66
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1827 bonds, 75 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> undo
> nucleotides sel ladder
> cartoon hide sel
> style sel stick
Changed 1639 atom styles
> nucleotides sel atoms
> cartoon sel
> select clear
> show #!1 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #!2 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker beta_no1_cl3_rsr_real_space_refined.pdb, chain 2 (#1) with
beta_no1_cl2_rsr_real_space_refined 1.pdb, chain 2 (#2), sequence alignment
score = 7175.2
RMSD between 1752 pruned atom pairs is 0.739 angstroms; (across all 1798
pairs: 0.821)
> show #!1 models
> matchmaker #!2 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker beta_no1_cl3_rsr_real_space_refined.pdb, chain 2 (#1) with
beta_no1_cl2_rsr_real_space_refined 1.pdb, chain 2 (#2), sequence alignment
score = 7175.2
RMSD between 1752 pruned atom pairs is 0.739 angstroms; (across all 1798
pairs: 0.821)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show "Side View"
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> lighting simple
> lighting soft
> show #!2 models
> hide #!1 models
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting simple
> lighting full
> lighting simple
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> save C:\WINDOWS\system32\image1.png supersample 3
Permission denied writing file C:\WINDOWS\system32\image1.png
> show #!1 models
> hide #!2 models
> save C:\WINDOWS\system32\image1.png supersample 3
Permission denied writing file C:\WINDOWS\system32\image1.png
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/Laura_figures/beta_conformation1.png" width 941
> height 580 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/Laura_figures/beta_conformation2.png" width 941
> height 580 supersample 3 transparentBackground true
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
Chain information for PIN_5_real_space_refined.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
> select add #3
104236 atoms, 109969 bonds, 31 pseudobonds, 10152 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #3/m:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 16 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> select up
1141 atoms, 1164 bonds, 148 residues, 1 model selected
> select up
104236 atoms, 109969 bonds, 10152 residues, 1 model selected
> select down
1141 atoms, 1164 bonds, 148 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!3 to #2/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker beta_no1_cl2_rsr_real_space_refined 1.pdb, chain 2 (#2) with
PIN_5_real_space_refined.pdb, chain 2 (#3), sequence alignment score = 7069.4
RMSD between 1709 pruned atom pairs is 0.717 angstroms; (across all 1780
pairs: 1.252)
> select clear
> select #3/l
1037 atoms, 1051 bonds, 3 pseudobonds, 129 residues, 2 models selected
> select ~sel & ##selected
103199 atoms, 108918 bonds, 28 pseudobonds, 10023 residues, 2 models selected
> hide sel cartoons
> select #3/l:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
82 atoms, 82 bonds, 10 residues, 1 model selected
> select up
403 atoms, 412 bonds, 51 residues, 1 model selected
> select up
414 atoms, 422 bonds, 52 residues, 1 model selected
> select down
403 atoms, 412 bonds, 51 residues, 1 model selected
> select clear
> select #3/l
1037 atoms, 1051 bonds, 3 pseudobonds, 129 residues, 2 models selected
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #000099ff
> color (#!3 & sel) #009966ff
> select clear
> select #2/1:46
24 atoms, 26 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1827 bonds, 75 residues, 1 model selected
> select up
86939 atoms, 92347 bonds, 7918 residues, 1 model selected
> select #2/1:7
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1639 atoms, 1827 bonds, 75 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime green
> color sel green
> select clear
> open "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/6gsn.cif"
6gsn.cif title:
Structure of a partial yeast 48S preinitiation complex in closed conformation
[more info...]
Chain information for 6gsn.cif #4
---
Chain | Description | UniProt
1 | tRNAi (75-MER) |
2 | 18S rRNA (1798-MER) |
3 | mRNA |
A | 40S ribosomal protein S0 | RSSA_KLULA 2-220
B | 40S ribosomal protein S1 | RS3A_KLULA 3-233
C | KLLA0F09812p | Q6CKL3_KLULA 39-255
D | KLLA0D08305p | Q6CRK7_KLULA 3-225
E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 2-261
F | KLLA0D10659p | Q6CRA3_KLULA 22-227
G | 40S ribosomal protein S6 | RS6_KLULA 1-226
H | 40S ribosomal protein S7 | Q6CTD6_KLULA 4-187
I | 40S ribosomal protein S8 | Q6CMG3_KLULA 2-201
J | KLLA0E23673p | Q6CM18_KLULA 2-183
K | KLLA0B08173p | Q6CVZ5_KLULA 1-96
L | KLLA0A10483p | Q6CX80_KLULA 2-156
M | 40S ribosomal protein S12 | Q6CLU4_KLULA 17-134
N | KLLA0F18040p | Q6CJK0_KLULA 2-151
O | 40S ribosomal protein S14 | RS14_KLULA 11-137
P | KLLA0F07843p | Q6CKV4_KLULA 13-129
Q | 40S ribosomal protein S16 | RS16_KLULA 3-143
R | KLLA0B01474p | Q6CWU3_KLULA 2-131
S | KLLA0B01562p | Q6CWT9_KLULA 2-146
T | KLLA0A07194p | Q6CXM0_KLULA 2-144
U | KLLA0F25542p | Q6CIM1_KLULA 15-120
V | 40S ribosomal protein S21 | RS21_KLULA 1-87
W | 40S ribosomal protein S22 | RS22_KLULA 2-130
X | RPS23 | Q875M3_KLULC 2-145
Y | 40S ribosomal protein S24 | Q6CU44_KLULA 2-135
Z | KLLA0B06182p | Q6CW78_KLULA 36-105
a | 40S ribosomal protein S26 | Q6CS01_KLULA 2-99
b | 40S ribosomal protein S27 | Q6CNL2_KLULA 2-82
c | 40S ribosomal protein S28 | RS28_KLULA 6-67
d | 40S ribosomal protein S29 | RS29_KLULA 4-56
e | 40S ribosomal protein S30 | Q6CUH5_KLULA 4-61
f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 82-150
g | KLLA0E12277p | Q6CNI7_KLULA 3-326
h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25
i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 5-115
j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST
3-265
k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST
90-519
l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST
127-270
m | Eukaryotic translation initiation factor eIF-1 | SUI1_YEAST 19-108
o | Eukaryotic translation initiation factor 3 subunit A,eIF3a | EIF3A_YEAST
5-492
p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 72-737
q | Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 96-794
r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAS7 48-96
s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAS7 1-342
Non-standard residues in 6gsn.cif #4
---
GCP — phosphomethylphosphonic acid guanylate ester
MET — methionine
MG — magnesium ion
ZN — zinc ion
> show #!2-4 cartoons
> hide #!2-4 atoms
> select #4/p:727
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
212 atoms, 214 bonds, 24 residues, 1 model selected
> select up
292 atoms, 298 bonds, 33 residues, 1 model selected
> select add #4/p:227
298 atoms, 303 bonds, 34 residues, 1 model selected
> select up
451 atoms, 456 bonds, 59 residues, 1 model selected
> select up
5147 atoms, 5282 bonds, 658 residues, 1 model selected
> select up
103798 atoms, 109571 bonds, 10079 residues, 1 model selected
> select up
381877 atoms, 404200 bonds, 36063 residues, 4 models selected
> select down
103798 atoms, 109571 bonds, 10079 residues, 79 models selected
> select down
5147 atoms, 5282 bonds, 658 residues, 1 model selected
> select down
451 atoms, 456 bonds, 59 residues, 1 model selected
> select up
5147 atoms, 5282 bonds, 658 residues, 1 model selected
> hide sel cartoons
> hide #!3 models
> show sel cartoons
> select clear
> select #4/p:649
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
41 atoms, 40 bonds, 5 residues, 1 model selected
> select up
4682 atoms, 4811 bonds, 593 residues, 1 model selected
> hide sel cartoons
> select #4/s:191
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
50 atoms, 50 bonds, 6 residues, 1 model selected
> select up
2019 atoms, 2064 bonds, 258 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!1 to #4/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6gsn.cif, chain 2 (#4) with
beta_no1_cl3_rsr_real_space_refined.pdb, chain 2 (#1), sequence alignment
score = 7141.6
RMSD between 1623 pruned atom pairs is 0.978 angstroms; (across all 1798
pairs: 1.364)
> hide #!2 models
> show #!1 models
> select #4/m:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
73 atoms, 73 bonds, 9 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> select up
103798 atoms, 109571 bonds, 10079 residues, 1 model selected
> select down
716 atoms, 724 bonds, 90 residues, 1 model selected
> select ~sel & ##selected
103082 atoms, 108847 bonds, 1737 pseudobonds, 9989 residues, 4 models selected
> color (#!4 & sel) cyan
> undo
> hide sel cartoons
> select #4/m:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
73 atoms, 73 bonds, 9 residues, 1 model selected
> select up
716 atoms, 724 bonds, 90 residues, 1 model selected
> color sel cyan
> select clear
> show #!3 models
> matchmaker #!4 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker beta_no1_cl3_rsr_real_space_refined.pdb, chain 2 (#1) with
6gsn.cif, chain 2 (#4), sequence alignment score = 7141.6
RMSD between 1623 pruned atom pairs is 0.978 angstroms; (across all 1798
pairs: 1.364)
> matchmaker #!3 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker beta_no1_cl3_rsr_real_space_refined.pdb, chain 2 (#1) with
PIN_5_real_space_refined.pdb, chain 2 (#3), sequence alignment score = 7069.4
RMSD between 1689 pruned atom pairs is 0.699 angstroms; (across all 1780
pairs: 1.265)
> matchmaker #!2 to #1/2 pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker beta_no1_cl3_rsr_real_space_refined.pdb, chain 2 (#1) with
beta_no1_cl2_rsr_real_space_refined 1.pdb, chain 2 (#2), sequence alignment
score = 7175.2
RMSD between 1752 pruned atom pairs is 0.739 angstroms; (across all 1798
pairs: 0.821)
> select #3/m:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 16 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> select ~sel & ##selected
103096 atoms, 108805 bonds, 31 pseudobonds, 10005 residues, 2 models selected
> hide sel cartoons
> select #3/m:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 16 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> color sel #000099ff
> color sel #009966ff
> select clear
> select #3/m:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 16 residues, 1 model selected
> select up
1140 atoms, 1164 bonds, 147 residues, 1 model selected
> surface sel
> surface hidePatches (#!3 & sel)
> select add #4/m:93
1148 atoms, 1171 bonds, 148 residues, 3 models selected
> select up
1213 atoms, 1237 bonds, 156 residues, 3 models selected
> select up
1856 atoms, 1888 bonds, 237 residues, 3 models selected
> surface (#!3-4 & sel)
> select clear
> select #1/k:515
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
79 atoms, 82 bonds, 9 residues, 2 models selected
> select up
3596 atoms, 3657 bonds, 470 residues, 2 models selected
> select up
3604 atoms, 3664 bonds, 471 residues, 2 models selected
> hide sel cartoons
> select #1/j:209
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
104 atoms, 103 bonds, 14 residues, 2 models selected
> select up
683 atoms, 689 bonds, 90 residues, 2 models selected
> select up
705 atoms, 711 bonds, 93 residues, 2 models selected
> select up
2145 atoms, 2177 bonds, 267 residues, 2 models selected
> hide sel cartoons
> select #1/i:110@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
77 atoms, 77 bonds, 11 residues, 2 models selected
> select up
764 atoms, 773 bonds, 95 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select clear
> select #1/i:57
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 2 models selected
> select up
764 atoms, 773 bonds, 95 residues, 2 models selected
> surface (#!1 & sel)
> select clear
> save C:\WINDOWS\system32\image1.png supersample 3
Permission denied writing file C:\WINDOWS\system32\image1.png
> cd C:/ProgramData/ChimeraX
Current working directory is: C:\ProgramData\ChimeraX
> save C:\ProgramData\ChimeraX\image350.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/new_session_files/2beta_TC_conformations_new_cl3.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select #1/j
2145 atoms, 2177 bonds, 1 pseudobond, 267 residues, 2 models selected
> show sel cartoons
> select clear
> ui tool show "Side View"
> save C:\ProgramData\ChimeraX\image351.png supersample 3
> save "D:/PhD common folder/OneDrive - Indian Institute of
> Science/Jose_TH_43S_PIC/New_RSR_models/new_session_files/2beta_TC_conformations_new_cl3.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 136, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 457.49
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_IN.cp1252
Qt version: PyQt6 6.5.1, Qt 6.5.1
Qt runtime version: 6.5.1
Qt platform: windows
Manufacturer: LENOVO
Model: 82B5
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 8,452,902,912
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.7.22
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46.1
ChimeraX-AtomicLibrary: 10.0.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.4
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307220101
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.31.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.41.1
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.9.1
prompt-toolkit: 3.0.39
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.5.1
PyQt6-Qt6: 6.5.1
PyQt6-sip: 13.5.1
PyQt6-WebEngine-commercial: 6.5.0
PyQt6-WebEngine-Qt6: 6.5.1
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
WMI: 1.5.1
Change History (3)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving session |
comment:2 by , 2 years ago
| Status: | assigned → feedback |
|---|
It's unclear where the memory has gone. Can you reproduce this easily? And if so how?
A temporary solution might be to restart ChimeraX occasionally. But depending on how much data you're working with, you might need to work on a computer with more memory.
comment:3 by , 2 years ago
I think this is a bug in the Python lz4 compression module. We have seen it reported about 5 times. We are using the latest lz4 version 4.3.2 from December 2022. So I don't think there is any way for us to fix this.
For working with large atomic models and maps having only 8 Gbytes of memory is asking for these kinds of problems. I would recommend at least 16 Gbytes for working with large data.
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Reported by Prafful Sharma