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Opened 4 years ago
Closed 4 years ago
#6322 closed defect (can't reproduce)
Bad pseudobond / group attributes
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\Hevle001\\\Desktop\\\Respirasome_manuscript\\\alternative_cox_position.cxs
Log from Tue Mar 1 16:31:55 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\Hevle001\\\Desktop\\\Respirasome_manuscript\\\xlinked_subunits_w_alternative_cox_respirasome.cxs
Log from Mon Feb 28 13:21:05 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\Hevle001\\\Desktop\\\Respirasome_manuscript\\\respirasome_for_images_w_xlinks.cxs
Log from Mon Feb 28 12:28:37 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\Hevle001\\\Desktop\\\Respirasome_manuscript\\\structural_analysis\\\Mapping_xlinks\\\chimera_sessions\\\Respirasome_model_w_xlinked_mouse_subunits_alphafold_with_MouseEMstructuresOverlaid-5gpn.cxs
Log from Tue Feb 8 14:13:04 2022UCSF ChimeraX version: 1.3.dev202110120902
(2021-10-12)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_w_MouseEMstructuresOverlaid2-IC.cxs
Log from Mon Feb 7 11:51:19 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_w_MouseEMstructuresOverlaid2-IC.cxs
Log from Mon Feb 7 11:42:53 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_w_MouseEMstructuresOverlaid-
> IC.cxs
Log from Tue Feb 1 15:37:03 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold.cxs
Log from Sun Jan 30 19:31:02 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> D:\\\Projects\\\15_Respirasome\\\Resp_MS1_analysis_for_manuscript\\\Analysis_respirasome\\\raw_extracted_xlinks_for_complexes\\\chimera_mapping_respirasome\\\Mapping_xlinks_onto_respirasome.cxs
Log from Tue Dec 14 14:13:55 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:\Projects\15_Respirasome\New_analysis\Analysis_respirasome\xlinked_subunits.pdb
> format pdb
Chain information for xlinked_subunits.pdb #1
---
Chain | Description
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
> hide atoms
> show cartoons
> set bgColor white
> ui tool show XMAS
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_inter_respirasome_xl.xlsx
Unique peptide pairs: 25 out of 25
Unique peptide pairs with pseudobonds: 25
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_inter_respirasome_xl_1.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_inter_respirasome_xl_filtered.xlsx
Traceback (most recent call last):
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\indexes\base.py", line 3361, in get_loc
return self._engine.get_loc(casted_key)
File "pandas\\_libs\index.pyx", line 76, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\index.pyx", line 108, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'Sequence A'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\xmas\tool.py", line 107, in <lambda>
map_button.clicked.connect(lambda: self.map_button_clicked(
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\xmas\tool.py", line 459, in map_button_clicked
self.map_crosslinks(
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\xmas\tool.py", line 485, in map_crosslinks
input_peptides_A = dataframe["Sequence A"].tolist()
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\frame.py", line 3458, in __getitem__
indexer = self.columns.get_loc(key)
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\indexes\base.py", line 3363, in get_loc
raise KeyError(key) from err
KeyError: 'Sequence A'
KeyError: 'Sequence A'
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\indexes\base.py", line 3363, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_inter_respirasome_xl.xlsx
Unique peptide pairs: 31 out of 31
Unique peptide pairs with pseudobonds: 31
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_inter_respirasome_xl_1.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_inter_respirasome_xl_filtered.xlsx
Unique peptide pairs: 15 out of 15
Unique peptide pairs with pseudobonds: 15
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_inter_respirasome_xl_filtered_1.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_inter_respirasome_xl_filtered.xlsx
Traceback (most recent call last):
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\indexes\base.py", line 3361, in get_loc
return self._engine.get_loc(casted_key)
File "pandas\\_libs\index.pyx", line 76, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\index.pyx", line 108, in
pandas._libs.index.IndexEngine.get_loc
File "pandas\\_libs\hashtable_class_helper.pxi", line 5198, in
pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas\\_libs\hashtable_class_helper.pxi", line 5206, in
pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'Sequence A'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\xmas\tool.py", line 107, in <lambda>
map_button.clicked.connect(lambda: self.map_button_clicked(
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\xmas\tool.py", line 459, in map_button_clicked
self.map_crosslinks(
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\chimerax\xmas\tool.py", line 485, in map_crosslinks
input_peptides_A = dataframe["Sequence A"].tolist()
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\frame.py", line 3458, in __getitem__
indexer = self.columns.get_loc(key)
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\indexes\base.py", line 3363, in get_loc
raise KeyError(key) from err
KeyError: 'Sequence A'
KeyError: 'Sequence A'
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.2\site-
packages\pandas\core\indexes\base.py", line 3363, in get_loc
raise KeyError(key) from err
See log for complete Python traceback.
QCoreApplication::exec: The event loop is already running
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_inter_respirasome_xl_filtered.xlsx
Unique peptide pairs: 16 out of 16
Unique peptide pairs with pseudobonds: 16
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_inter_respirasome_xl_filtered_1.pb
QCoreApplication::exec: The event loop is already running
QCoreApplication::exec: The event loop is already running
QCoreApplication::exec: The event loop is already running
QCoreApplication::exec: The event loop is already running
> select clear
> open 5GUP
Summary of feedback from opening 5GUP fetched from pdb
---
warnings | Atom OG has no neighbors to form bonds with according to residue
template for SER /2:79
Atom OG has no neighbors to form bonds with according to residue template for
SER /4:79
5gup title:
Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 [more
info...]
Chain information for 5gup #10
---
Chain | Description
0 Ab | Cytochrome b-c1 complex subunit 6, mitochondrial
1 Ac | Cytochrome b-c1 complex subunit 9
2 4 | Cytochrome b-c1 complex subunit Rieske, mitochondrial
3 Ad | Cytochrome b-c1 complex subunit 10
5 u | Cytochrome b-c1 complex subunit 1, mitochondrial
6 v | Cytochrome b-c1 complex subunit 2, mitochondrial
7 w | Cytochrome b
8 x | Cytochrome c1, heme protein, mitochondrial
9 y | Cytochrome b-c1 complex subunit 7
A | Cytochrome c oxidase subunit 6C
Aa z | Cytochrome b-c1 complex subunit 8
Ae Af | Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Ag | Cytochrome c oxidase subunit 8B, mitochondrial
Ah | Cytochrome c oxidase subunit 7A1, mitochondrial
Ai | Cytochrome c oxidase subunit 7B, mitochondrial
Aj | Cytochrome c oxidase subunit 7C, mitochondrial
Ak | Cytochrome c oxidase subunit 1
Al | Cytochrome c oxidase subunit 2
Am | Cytochrome c oxidase subunit 3
An | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Ao | Cytochrome c oxidase subunit 5A, mitochondrial
Ap | Cytochrome c oxidase subunit 5B, mitochondrial
Aq | Cytochrome c oxidase subunit 6A, mitochondrial
Ar | Cytochrome c oxidase subunit 6B1
B | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
H | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
J | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
K R | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12
L | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial
M | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7
N | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5
O X | Acyl carrier protein, mitochondrial
P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2
Q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6
S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1
T | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3
U | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial
V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11
W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13
Y | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial
Z | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3
a | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial
b | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6
c | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial
d | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10
e | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial
f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
g | NADH dehydrogenase [ubiquinone] 1 subunit C2
h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
i | NADH-ubiquinone oxidoreductase chain 2
j | NADH-ubiquinone oxidoreductase chain 3
k | NADH-ubiquinone oxidoreductase chain 4L
l | NADH-ubiquinone oxidoreductase chain 5
m | NADH-ubiquinone oxidoreductase chain 6
n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1
o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4
p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9
q | NADH-ubiquinone oxidoreductase chain 4
r | NADH-ubiquinone oxidoreductase chain 1
s | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8
t | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7
Non-standard residues in 5gup #10
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
PEE — 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol
SF4 — iron/sulfur cluster
ZMP — S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-
alanyl}amino)ethyl] tetradecanethioate
ZN — zinc ion
> hide atoms
> show cartoons
> crosslinks
Missing or invalid "pbonds" argument: empty atom specifier
> crosslinks #5-9 dashes 0
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #8 models
> hide #9 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> transparency #1 50 cartoons s
Expected ',' or a keyword
> transparency #1 50 cs
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #1 50 cartoons s
Expected ',' or a keyword
> transparency #1 50 cartoons,surfaces
> hide #!10 models
> show #7 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> show #!10 models
> transparency #10 80 cartoons,surfaces
> hide #1 models
> show #1 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #7 models
> show #6 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #6 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #8 models
> show #9 models
> hide #9 models
> hide #8 models
> show #9 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!10 models
> save
> D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/Mapping_xlinks_onto_respirasome.cxs
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
QCoreApplication::exec: The event loop is already running
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_all.xlsx
Unique peptide pairs: 6 out of 6
Unique peptide pairs with pseudobonds: 6
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_all_1,10.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_filtered.xlsx
Unique peptide pairs: 7 out of 7
Unique peptide pairs with pseudobonds: 7
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_filtered_1,10.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_all.xlsx
Unique peptide pairs: 12 out of 12
Unique peptide pairs with pseudobonds: 12
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_all_1,10.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_filtered.xlsx
Unique peptide pairs: 6 out of 6
Unique peptide pairs with pseudobonds: 6
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_filtered_1,10.pb
QCoreApplication::exec: The event loop is already running
QCoreApplication::exec: The event loop is already running
> close #11-18
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_all.xlsx
Unique peptide pairs: 6 out of 6
Unique peptide pairs with pseudobonds: 6
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_all_1.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_filtered.xlsx
Unique peptide pairs: 7 out of 7
Unique peptide pairs with pseudobonds: 7
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/ki_unique_respirasome_inter_xl_filtered_1.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_all.xlsx
Unique peptide pairs: 12 out of 12
Unique peptide pairs with pseudobonds: 12
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_all_1.pb
Peptide pair mapping of PD output file:
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_filtered.xlsx
Unique peptide pairs: 6 out of 6
Unique peptide pairs with pseudobonds: 6
Pseudobonds opened from
D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/wt_unique_respirasome_inter_xl_filtered_1.pb
QCoreApplication::exec: The event loop is already running
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #8 models
> hide #9 models
> hide #16 models
> hide #18 models
> select clear
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> crosslinks #15-18 dashes 0
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> hide #17 models
> show #16 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> save
> D:/Projects/15_Respirasome/New_analysis/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/Mapping_xlinks_onto_respirasome.cxs
——— End of log from Tue Dec 14 14:13:55 2021 ———
opened ChimeraX session
> close #11-18
> close #2-9
> show #!10 models
> hide #!10 models
> save
> D:/Projects/15_Respirasome/Resp_MS1_analysis_for_manuscript/Analysis_respirasome/raw_extracted_xlinks_for_complexes/chimera_mapping_respirasome/mapped_xl_tables/Respirasome_model_w_xlinked_mouse_subunits_alphafold.cxs
——— End of log from Sun Jan 30 19:31:02 2022 ———
opened ChimeraX session
> show #!10 models
> hide #!10 models
> show #!10 models
> open /Users/ic356/Downloads/Mouse_CIII2_focus_7o3h_Vercellino2021.cif
Summary of feedback from opening
/Users/ic356/Downloads/Mouse_CIII2_focus_7o3h_Vercellino2021.cif
---
notes | Fetching CCD HEM from http://ligand-
expo.rcsb.org/reports/H/HEM/HEM.cif
Fetching CCD HEC from http://ligand-expo.rcsb.org/reports/H/HEC/HEC.cif
Fetching CCD PC1 from http://ligand-expo.rcsb.org/reports/P/PC1/PC1.cif
Mouse_CIII2_focus_7o3h_Vercellino2021.cif title:
Murine CIII2 focus-refined from supercomplex CICIII2 [more info...]
Chain information for Mouse_CIII2_focus_7o3h_Vercellino2021.cif #2
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | Cytochrome b | CYB_MOUSE
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE
K V | Cytochrome b-c1 complex subunit 10 | QCR10_MOUSE
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE
Non-standard residues in Mouse_CIII2_focus_7o3h_Vercellino2021.cif #2
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
FES — FE2/S2 (inorganic) cluster
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> open
> /Users/ic356/Downloads/Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif
Summary of feedback from opening
/Users/ic356/Downloads/Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif
---
notes | Fetching CCD TGL from http://ligand-
expo.rcsb.org/reports/T/TGL/TGL.cif
Fetching CCD CU from http://ligand-expo.rcsb.org/reports/C/CU/CU.cif
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif
Fetching CCD HEA from http://ligand-expo.rcsb.org/reports/H/HEA/HEA.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD CUA from http://ligand-expo.rcsb.org/reports/C/CUA/CUA.cif
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif title:
Murine supercomplex CIII2CIV in the assembled locked conformation [more
info...]
Chain information for
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif #3
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | Cytochrome b | CYB_MOUSE
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE
I | Cox7a2l protein | Q99KD6_MOUSE
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE
K V | Cytochrome b-c1 complex subunit 10 | QCR10_MOUSE
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE
a | Cytochrome c oxidase subunit 1 | COX1_MOUSE
b | Cytochrome c oxidase subunit 2 | COX2_MOUSE
c | Cytochrome c oxidase subunit 3 | COX3_MOUSE
d | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
e | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_MOUSE
f | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_MOUSE
g | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_MOUSE
h | Cytochrome c oxidase subunit 6B1 | CX6B1_MOUSE
i | Cytochrome c oxidase subunit 6C | COX6C_MOUSE
k | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_MOUSE
l | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_MOUSE
m | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_MOUSE
Non-standard residues in
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif #3
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
FES — FE2/S2 (inorganic) cluster
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NA — sodium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
TGL — tristearoylglycerol (triacylglycerol)
ZN — zinc ion
> open
> /Users/ic356/Downloads/Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif title:
Murine supercomplex CIII2CIV in the intermediate locked conformation [more
info...]
Chain information for
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif #4
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | Cytochrome b | CYB_MOUSE
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE
I | Cox7a2l protein | Q99KD6_MOUSE
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE
P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE
a | Cytochrome c oxidase subunit 1 | COX1_MOUSE
b | Cytochrome c oxidase subunit 2 | COX2_MOUSE
c | Cytochrome c oxidase subunit 3 | COX3_MOUSE
d | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
e | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_MOUSE
f | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_MOUSE
g | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_MOUSE
h | Cytochrome c oxidase subunit 6B1 | CX6B1_MOUSE
i | Cytochrome c oxidase subunit 6C | COX6C_MOUSE
k | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_MOUSE
l | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_MOUSE
m | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_MOUSE
Non-standard residues in
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif #4
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NA — sodium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
TGL — tristearoylglycerol (triacylglycerol)
ZN — zinc ion
> open
> /Users/ic356/Downloads/Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif title:
Murine supercomplex CIII2CIV in the mature unlocked conformation [more
info...]
Chain information for Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif
#5
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | Cytochrome b | CYB_MOUSE
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE
I | Cox7a2l protein | Q99KD6_MOUSE
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE
K V | Cytochrome b-c1 complex subunit 10 | QCR10_MOUSE
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE
a | Cytochrome c oxidase subunit 1 | COX1_MOUSE
b | Cytochrome c oxidase subunit 2 | COX2_MOUSE
c | Cytochrome c oxidase subunit 3 | COX3_MOUSE
d | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
e | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_MOUSE
f | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_MOUSE
g | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_MOUSE
h | Cytochrome c oxidase subunit 6B1 | CX6B1_MOUSE
i | Cytochrome c oxidase subunit 6C | COX6C_MOUSE
k | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_MOUSE
l | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_MOUSE
m | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_MOUSE
Non-standard residues in
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif #5
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
FES — FE2/S2 (inorganic) cluster
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NA — sodium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
TGL — tristearoylglycerol (triacylglycerol)
ZN — zinc ion
> hide atoms
> show cartoons
> undo
> show #2-5 cartoons
> select #2-5 model
Expected a keyword
> select #2-5 models
Expected a keyword
> select !#2-5 models
Expected an objects specifier or a keyword
> select !#2-5 model
Expected an objects specifier or a keyword
> select !#2-5
Expected an objects specifier or a keyword
> select !#2-5 models
Expected an objects specifier or a keyword
Drag select of 21515 residues, 1 pseudobonds
> ui tool show "Fit in Map"
> select #2
33700 atoms, 34505 bonds, 43 pseudobonds, 4185 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!2 models
> mmaker #3-5/C to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain C (#2) with
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif, chain C (#3),
sequence alignment score = 1992.4
RMSD between 379 pruned atom pairs is 0.270 angstroms; (across all 379 pairs:
0.270)
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain C (#2) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain C (#4),
sequence alignment score = 1983.4
RMSD between 360 pruned atom pairs is 0.718 angstroms; (across all 379 pairs:
0.960)
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain C (#2) with
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif, chain C (#5),
sequence alignment score = 1994.8
RMSD between 379 pruned atom pairs is 0.282 angstroms; (across all 379 pairs:
0.282)
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> select #2
33700 atoms, 34505 bonds, 43 pseudobonds, 4185 residues, 2 models selected
> select #5
48532 atoms, 49783 bonds, 76 pseudobonds, 6008 residues, 2 models selected
> ~select #5
Nothing selected
Drag select of 4161 residues
> select #2
33700 atoms, 34505 bonds, 43 pseudobonds, 4185 residues, 2 models selected
> ~select #2
Nothing selected
> colour #10 bychain cartoon
> hide #1 models
> colour #10 bychain cartoon
> mmaker #2-5/C to #1/7
No 'to' model specified
> mmaker #2-5/C to #10/7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gup, chain 7 (#10) with Mouse_CIII2_focus_7o3h_Vercellino2021.cif,
chain C (#2), sequence alignment score = 1757
RMSD between 370 pruned atom pairs is 0.834 angstroms; (across all 378 pairs:
0.923)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif, chain C (#3),
sequence alignment score = 1766.6
RMSD between 369 pruned atom pairs is 0.810 angstroms; (across all 378 pairs:
0.906)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain C (#4),
sequence alignment score = 1757.6
RMSD between 344 pruned atom pairs is 0.953 angstroms; (across all 378 pairs:
1.209)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif, chain C (#5),
sequence alignment score = 1749.2
RMSD between 369 pruned atom pairs is 0.837 angstroms; (across all 378 pairs:
0.923)
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!10 models
> show #!10 models
> show #!5 models
> mmaker #2-5/N to #10/7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gup, chain 7 (#10) with Mouse_CIII2_focus_7o3h_Vercellino2021.cif,
chain N (#2), sequence alignment score = 1782.8
RMSD between 367 pruned atom pairs is 0.836 angstroms; (across all 378 pairs:
0.951)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif, chain N (#3),
sequence alignment score = 1742
RMSD between 368 pruned atom pairs is 0.809 angstroms; (across all 378 pairs:
0.916)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain N (#4),
sequence alignment score = 1723.4
RMSD between 331 pruned atom pairs is 0.925 angstroms; (across all 378 pairs:
1.463)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif, chain N (#5),
sequence alignment score = 1776.8
RMSD between 368 pruned atom pairs is 0.809 angstroms; (across all 378 pairs:
0.920)
> show #!4 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!2 models
> show #!5 models
> hide #!2 models
> show #!4 models
> hide #!10 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> mmaker #2-5/C to #10/7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gup, chain 7 (#10) with Mouse_CIII2_focus_7o3h_Vercellino2021.cif,
chain C (#2), sequence alignment score = 1757
RMSD between 370 pruned atom pairs is 0.834 angstroms; (across all 378 pairs:
0.923)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif, chain C (#3),
sequence alignment score = 1766.6
RMSD between 369 pruned atom pairs is 0.810 angstroms; (across all 378 pairs:
0.906)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain C (#4),
sequence alignment score = 1757.6
RMSD between 344 pruned atom pairs is 0.953 angstroms; (across all 378 pairs:
1.209)
Matchmaker 5gup, chain 7 (#10) with
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif, chain C (#5),
sequence alignment score = 1749.2
RMSD between 369 pruned atom pairs is 0.837 angstroms; (across all 378 pairs:
0.923)
> show #!10 models
> show #!4 models
> hide #!4 models
Drag select of 1669 residues
> select clear
> hide #!10 models
> select #3/a-m
14003 atoms, 14429 bonds, 32 pseudobonds, 1722 residues, 2 models selected
> show #3/a-m surfaces
> undo
[Repeated 2 time(s)]
> hide #3/a-m surfaces
> hide ~/a-m & #3-5 surfaces
> hide ~/a-m & #3-5 cartoons
> show #!2 models
> hide #!2 models
> mmaker #3-5/f to #10/Ap
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gup, chain Ap (#10) with
Mouse_CIII2CIV_SC_assembledLocked_7o37_Vercellino2021.cif, chain f (#3),
sequence alignment score = 430.1
RMSD between 88 pruned atom pairs is 0.653 angstroms; (across all 95 pairs:
1.098)
Matchmaker 5gup, chain Ap (#10) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain f (#4),
sequence alignment score = 437.3
RMSD between 89 pruned atom pairs is 0.661 angstroms; (across all 95 pairs:
1.058)
Matchmaker 5gup, chain Ap (#10) with
Mouse_CIII2CIV_SC_matureUnlocked_7o3c_Vercellino2021.cif, chain f (#5),
sequence alignment score = 440.3
RMSD between 88 pruned atom pairs is 0.767 angstroms; (across all 95 pairs:
1.241)
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> colour #3-5 light blue cartoon
> transparency #10 0 cartoons
> show #!4 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> undo
[Repeated 6 time(s)]
> show #!4 models
> hide #!5 models
> transparency #10 90 cartoons
> transparency #10 80 cartoons
> transparency #10 70 cartoons
> show #!2 models
> open
> /Users/ic356/Downloads/Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif title:
Murine supercomplex CIII2CIV in the intermediate locked conformation [more
info...]
Chain information for
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif #6
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | Cytochrome b | CYB_MOUSE
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE
I | Cox7a2l protein | Q99KD6_MOUSE
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE
P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE
a | Cytochrome c oxidase subunit 1 | COX1_MOUSE
b | Cytochrome c oxidase subunit 2 | COX2_MOUSE
c | Cytochrome c oxidase subunit 3 | COX3_MOUSE
d | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
e | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_MOUSE
f | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_MOUSE
g | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_MOUSE
h | Cytochrome c oxidase subunit 6B1 | CX6B1_MOUSE
i | Cytochrome c oxidase subunit 6C | COX6C_MOUSE
k | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_MOUSE
l | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_MOUSE
m | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_MOUSE
Non-standard residues in
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif #6
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NA — sodium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
TGL — tristearoylglycerol (triacylglycerol)
ZN — zinc ion
> hide atoms
> show cartoons
> hide atoms
> show #6 cartoons
> hide #!10 models
> mmaker #6/C to #2/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain C (#2) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain C (#6),
sequence alignment score = 1983.4
RMSD between 360 pruned atom pairs is 0.718 angstroms; (across all 379 pairs:
0.960)
> mmaker #6/C to #4/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain
C (#4) with Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif,
chain C (#6), sequence alignment score = 2031.4
RMSD between 380 pruned atom pairs is 0.000 angstroms; (across all 380 pairs:
0.000)
> mmaker #6 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain
a (#4) with Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif,
chain a (#6), sequence alignment score = 2750.3
RMSD between 514 pruned atom pairs is 0.000 angstroms; (across all 514 pairs:
0.000)
> hide ~/a-m & #6 cartoons
> open /Users/ic356/Downloads/Mouse_CIII2_focus_7o3h_Vercellino2021.cif
Mouse_CIII2_focus_7o3h_Vercellino2021.cif title:
Murine CIII2 focus-refined from supercomplex CICIII2 [more info...]
Chain information for Mouse_CIII2_focus_7o3h_Vercellino2021.cif #7
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE
C N | Cytochrome b | CYB_MOUSE
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE
K V | Cytochrome b-c1 complex subunit 10 | QCR10_MOUSE
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE
Non-standard residues in Mouse_CIII2_focus_7o3h_Vercellino2021.cif #7
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
FES — FE2/S2 (inorganic) cluster
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> hide atoms
> show #7 cartoons
> mmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain A (#2) with
Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain A (#7), sequence alignment
score = 2329
RMSD between 446 pruned atom pairs is 0.000 angstroms; (across all 446 pairs:
0.000)
> mmaker #7/C to #2/N bring #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain N (#2) with
Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain C (#7), sequence alignment
score = 1976.8
RMSD between 377 pruned atom pairs is 0.260 angstroms; (across all 380 pairs:
0.354)
> hide #!7 models
> show #!10 models
> open /Users/ic356/Downloads/6zr2.pdb
6zr2.pdb title:
Cryo-em structure of respiratory complex I In the active state from mus
musculus At 3.1 A [more info...]
Chain information for 6zr2.pdb #8
---
Chain | Description | UniProt
A | NADH dehydrogenase subunit 3 | NU3M_MOUSE
B | nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial |
NDUS7_MOUSE
C | nadh dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial |
NDUS3_MOUSE
D | nadh dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial |
NDUS2_MOUSE
E | NADH-ubiquinone oxidoreductase 24 KDA subunit | NDUV2_MOUSE
F | nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial |
NDUV1_MOUSE
G | nadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial | NDUS1_MOUSE
H | NADH dehydrogenase subunit 1 | NU1M_MOUSE
I | nadh dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial |
NDUS8_MOUSE
J | NADH dehydrogenase subunit 6 | NU6M_MOUSE
K | NADH dehydrogenase subunit 4L | NU4LM_MOUSE
L | NADH dehydrogenase subunit 5 | NU5M_MOUSE
M | NADH dehydrogenase subunit 4 | NU4M_MOUSE
N | NADH dehydrogenase subunit 2 | NU2M_MOUSE
O | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial |
NDUAA_MOUSE
P | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial |
NDUA9_MOUSE
Q | nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial |
NDUS4_MOUSE
R | nadh dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial |
NDUS6_MOUSE
S | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 | NDUA2_MOUSE
T | acyl carrier protein, mitochondrial | ACPM_MOUSE
U | acyl carrier protein, mitochondrial | ACPM_MOUSE
V | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 | NDUA5_MOUSE
W | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 | NDUA6_MOUSE
X | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 | NDUA8_MOUSE
Y | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11 | G5E814_MOUSE
Z | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 | NDUAD_MOUSE
a | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 | NDUA1_MOUSE
b | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 | NDUA3_MOUSE
c | nadh dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | NDUC1_MOUSE
d | nadh dehydrogenase [ubiquinone] 1 subunit C2 | NDUC2_MOUSE
e | nadh dehydrogenase [ubiquinone] iron-sulfur protein 5 | NDUS5_MOUSE
f | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 | NDUB1_MOUSE
g | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial |
NDUBB_MOUSE
h | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial |
NDUB5_MOUSE
i | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 6 | NDUB6_MOUSE
j | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial |
NDUB2_MOUSE
k | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 | NDUB3_MOUSE
l | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial |
NDUB8_MOUSE
m | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 | NDUB4_MOUSE
n | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 | NDUB9_MOUSE
o | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 | NDUB7_MOUSE
p | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 | NDUBA_MOUSE
q | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 | NDUAC_MOUSE
r | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 7 | NDUA7_MOUSE
s | nadh dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial |
NDUV3_MOUSE
Non-standard residues in 6zr2.pdb #8
---
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)
ATP — adenosine-5'-triphosphate
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-
butanoyl]amino]propanoylamino]ethyl](3~{S})-3-oxidanyltetradecanethioate
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
NDP — nadph dihydro-nicotinamide-adenine-dinucleotidephosphate
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
SF4 — iron/sulfur cluster
ZN — zinc ion
> hide atoms
> show #8 cartoons
> select #8
67042 atoms, 68744 bonds, 38 pseudobonds, 8216 residues, 3 models selected
> ui mousemode right "translate selected models"
> hide #!6 models
> hide #!4 models
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.71767,-0.68469,-0.12711,592.54,0.39326,-0.24784,-0.88539,401.34,0.57471,-0.68541,0.44713,151.37
> view matrix models
> #8,-0.47933,-0.8162,-0.32259,612.57,-0.010525,0.37289,-0.92782,366.08,0.87757,-0.44134,-0.18733,175.44
> view matrix models
> #8,-0.48274,-0.80009,-0.35612,617.71,0.39636,0.163,-0.90351,311.61,0.78094,-0.57731,0.23843,127.73
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.48274,-0.80009,-0.35612,615.62,0.39636,0.163,-0.90351,304.29,0.78094,-0.57731,0.23843,157.32
> ~select #8
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!10 models
> ui mousemode right translate
> show #!10 models
> hide #!8 models
> show #!8 models
> mmaker #8/H to #10/m
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gup, chain m (#10) with 6zr2.pdb, chain H (#8), sequence alignment
score = 123.7
RMSD between 32 pruned atom pairs is 1.271 angstroms; (across all 168 pairs:
21.020)
> undo
> hide #!8 models
> colour #10 bychain cartoon
> mmaker #8 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gup, chain G (#10) with 6zr2.pdb, chain G (#8), sequence alignment
score = 3010.5
RMSD between 596 pruned atom pairs is 0.915 angstroms; (across all 673 pairs:
1.475)
> show #!8 models
> show #!2 models
> show #!6 models
> show #!4 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> hide #!4 models
> show #!4 models
> show #!8 models
> colour #2-8 gray cartoon
> transparency #2-8 50 cartoons
> hide #!10 models
> show #1 models
> hide #1 models
> save
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_w_MouseEMstructuresOverlaid-
> IC.cxs
——— End of log from Tue Feb 1 15:37:03 2022 ———
opened ChimeraX session
> colour #8/m,k,T,l,p,s,S,P,F#2/M,S,Q,L,A,B,F,H#4,6/l,f,d,e bychain cartoon
> transparency ~#8/m,k,T,l,p,s,S,P,F#2/M,S,Q,L,A,B,F,H#4,6/l,f,d,e & #8,2,4,6
> 90 cartoons
> save
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_w_MouseEMstructuresOverlaid1-IC.cxs
——— End of log from Mon Feb 7 11:42:53 2022 ———
opened ChimeraX session
> hide #!2 models
> hide #!4 models
> hide #!6 models
> hide #!8 models
> show #!10 models
> open /Users/ic356/Downloads/5gpn.cif
5gpn.cif title:
Architecture of mammalian respirasome [more info...]
Chain information for 5gpn.cif #9
---
Chain | Description | UniProt
0 | Cytochrome c oxidase subunit 3 |
1 | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_BOVIN
2 | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_BOVIN
3 | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_BOVIN
4 | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_BOVIN
5 | Cytochrome c oxidase subunit 6B1 | CX6B1_BOVIN
6 | Cytochrome c oxidase subunit 6C | COX6C_BOVIN
7 | Cytochrome c oxidase subunit 7A1, mitochondrial | CX7A1_BOVIN
8 | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_BOVIN
9 | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_BOVIN
A M | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_BOVIN
Aa t | Acyl carrier protein | F1SAB6_PIG
Ab Ah | NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment |
Ac | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 | K7GR43_PIG
Ad Ao Ap Av | NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment |
Ae | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 | F1SLY2_PIG
Af | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 | F1SRG2_PIG
Ag | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11 | I3LGM4_PIG
Ai u | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5 | F1SGC6_PIG
Aj | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 | I3LDC3_PIG
Ak | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9 | K7GSE5_PIG
Al | NADH dehydrogenase [ubiquinone] 1 subunit C2 | F1STY1_PIG
Am | NADH dehydrogenase [ubiquinone] 1 subunit C1 | F1RRC9_PIG
An | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 | F1SLR1_PIG
Aq As Aw | NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment |
Ar | NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment |
At | NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment |
Au | NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment |
B N | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_BOVIN
C O | Cytochrome b | CYB_BOVIN
D P | Cytochrome c1, heme protein, mitochondrial | CY1_BOVIN
E Q | Cytochrome b-c1 complex subunit Rieske, mitochondrial |
F R | Cytochrome b-c1 complex subunit 7 |
G S | Cytochrome b-c1 complex subunit 8 | QCR8_BOVIN
H T | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_BOVIN
I U | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_BOVIN
J L | Cytochrome b-c1 complex subunit 9 | QCR9_BOVIN
K V | Cytochrome b-c1 complex subunit 10 | QCR10_BOVIN
W | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 | F1SIF2_PIG
Y | NADH-ubiquinone oxidoreductase 75 kDa subunit | F1SHD7_PIG
Z | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 | F1S1A8_PIG
a | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7 | I3LK43_PIG
b | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 |
c | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial | F1RVN1_PIG
d | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial | F1SM98_PIG
e | NADH-ubiquinone oxidoreductase chain 1 | NU1M_PIG
f | NADH-ubiquinone oxidoreductase chain 2 | NU2M_PIG
g | NADH-ubiquinone oxidoreductase chain 3 | NU3M_PIG
h | NADH-ubiquinone oxidoreductase chain 4 | NU4M_PIG
i | NADH-ubiquinone oxidoreductase chain 4L | NU4LM_PIG
j | NADH-ubiquinone oxidoreductase chain 5 | NU5M_PIG
k l | NADH-ubiquinone oxidoreductase chain 6 | NU6M_PIG
m | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3 | F1RNI5_PIG
n | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 |
o | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 | F1SV23_PIG
p | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9 | F1SL07_PIG
q v | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial
| F1SIS9_PIG
r | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 | F1S6Q1_PIG
s | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_BOVIN
w | Mitochondrial NADH dehydrogenase Fe-S protein 4 | G8IFA6_PIG
x | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial |
F1S031_PIG
y | Cytochrome c oxidase subunit 1 | COX1_BOVIN
z | Cytochrome c oxidase subunit 2 | COX2_BOVIN
Non-standard residues in 5gpn.cif #9
---
CU — copper (II) ion
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
SF4 — iron/sulfur cluster
ZN — zinc ion
> hide atoms
> show #10 cartoons
> hide #!9 models
> hide #!10 models
> show #!9 models
> show #9 cartoons
> colour #9 gray cartoon
> transparency #9 90 cartoons
> show #!2 models
> hide #!2 models
> show #!8 models
> hide #!9 models
> show #!9 models
> mmaker #8 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gpn.cif, chain Y (#9) with 6zr2.pdb, chain G (#8), sequence
alignment score = 3018.3
RMSD between 596 pruned atom pairs is 0.915 angstroms; (across all 672 pairs:
1.474)
> hide #!9 models
> show #!9 models
> show #!2 models
> mmaker #2 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gpn.cif, chain M (#9) with
Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain L (#2), sequence alignment
score = 1964.6
RMSD between 419 pruned atom pairs is 0.768 angstroms; (across all 445 pairs:
1.705)
> show #!4 models
> mmaker #4/b to #9/z
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5gpn.cif, chain z (#9) with
Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain b (#4),
sequence alignment score = 1072.1
RMSD between 225 pruned atom pairs is 0.669 angstroms; (across all 227 pairs:
0.709)
> hide #!9 models
> show #!7 models
> hide #!7 models
> mmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain A (#2) with
Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain A (#7), sequence alignment
score = 2329
RMSD between 446 pruned atom pairs is 0.000 angstroms; (across all 446 pairs:
0.000)
> show #!6 models
> mmaker #6 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif, chain
a (#4) with Mouse_CIII2CIV_SC_intermediateLocked_7o3e_Vercellino2021.cif,
chain a (#6), sequence alignment score = 2750.3
RMSD between 514 pruned atom pairs is 0.000 angstroms; (across all 514 pairs:
0.000)
> show #!7 models
> hide #!4 models
> hide #!2 models
> hide #!6 models
> hide #!8 models
> colour #7 bychain cartoon
> show #!2 models
> show #!4 models
> show #!6 models
> show #!8 models
> mmaker #7/C to #2/N bring #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain N (#2) with
Mouse_CIII2_focus_7o3h_Vercellino2021.cif, chain C (#7), sequence alignment
score = 1976.8
RMSD between 377 pruned atom pairs is 0.260 angstroms; (across all 380 pairs:
0.354)
> hide #!7 models
> save
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_w_MouseEMstructuresOverlaid2-IC.cxs
——— End of log from Mon Feb 7 11:51:19 2022 ———
opened ChimeraX session
> colour #8/m,k,T,U,l,p,s,S,P,F#2/M,S,Q,L,A,B,F,H#4,6/l,f,d,e bychain cartoon
> transparency #8/m,k,T,U,l,p,s,S,P,F#2/M,S,Q,L,A,B,F,H#4,6/l,f,d,e 0 cartoons
> show #!9 models
> hide #!9 models
> rename #2 CIII2_pdb-7O3H
> close #3,5,7
> rename #4 CIV_pdb-7O3E id #3
> rename #6 CIV-alt_pdb-7O3E id #4
> rename #8 CI_pdb-6ZR2 id #5
> rename #9 5gpn id #6
> show #!6 models
> hide #!6 models
> save
> /Users/ic356/Downloads/xl_data_respirasome/Respirasome_model_w_xlinked_mouse_subunits_alphafold_with_MouseEMstructuresOverlaid-5gpn.cxs
——— End of log from Tue Feb 8 14:13:04 2022 ———
opened ChimeraX session
> show #!10 models
> show #!6 models
> hide #!6 models
> hide #!10 models
> show #1 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #1 models
> show #1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #1 models
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9DC69-ndufa9.pdb
AF-Q9DC69-ndufa9.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 α subcomplex
subunit 9, mitochondrial (Q9DC69) [more info...]
Chain information for AF-Q9DC69-ndufa9.pdb #7
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial |
NDUA9_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9DC70-ndufs7.pdb
AF-Q9DC70-ndufs7.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] iron- sulfur
protein 7, mitochondrial (Q9DC70) [more info...]
Chain information for AF-Q9DC70-ndufs7.pdb #8
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial |
NDUS7_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9DCS9-ndufb10.pdb
AF-Q9DCS9-ndufb10.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 β subcomplex
subunit 10 (Q9DCS9) [more info...]
Chain information for AF-Q9DCS9-ndufb10.pdb #9
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 10 | NDUBA_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q91YT0-nudfv1.pdb
AF-Q91YT0-nudfv1.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] flavoprotein 1,
mitochondrial (Q91YT0) [more info...]
Chain information for AF-Q91YT0-nudfv1.pdb #11
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial |
NDUV1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q8BK30-ndufv3.pdb
AF-Q8BK30-ndufv3.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] flavoprotein 3,
mitochondrial (Q8BK30) [more info...]
Chain information for AF-Q8BK30-ndufv3.pdb #12
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial |
NDUV3_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9CQ75-ndufa2.pdb
AF-Q9CQ75-ndufa2.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 α subcomplex
subunit 2 (Q9CQ75) [more info...]
Chain information for AF-Q9CQ75-ndufa2.pdb #13
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 | NDUA2_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9CQC7-ndufb4.pdb
AF-Q9CQC7-ndufb4.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 β subcomplex
subunit 4 (Q9CQC7) [more info...]
Chain information for AF-Q9CQC7-ndufb4.pdb #14
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 4 | NDUB4_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9CQH3-ndufb5.pdb
AF-Q9CQH3-ndufb5.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 β subcomplex
subunit 5, mitochondrial (Q9CQH3) [more info...]
Chain information for AF-Q9CQH3-ndufb5.pdb #15
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial |
NDUB5_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9CQZ6-ndufb3.pdb
AF-Q9CQZ6-ndufb3.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 β subcomplex
subunit 3 (Q9CQZ6) [more info...]
Chain information for AF-Q9CQZ6-ndufb3.pdb #16
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 3 | NDUB3_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9CR21-ndufab1.pdb
AF-Q9CR21-ndufab1.pdb title:
Alphafold V2.0 prediction for acyl carrier protein, mitochondrial (Q9CR21)
[more info...]
Chain information for AF-Q9CR21-ndufab1.pdb #17
---
Chain | Description | UniProt
A | acyl carrier protein, mitochondrial | ACPM_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexI/AF-Q9D6J5-ndufb8.pdb
AF-Q9D6J5-ndufb8.pdb title:
Alphafold V2.0 prediction for nadh dehydrogenase [ubiquinone] 1 β subcomplex
subunit 8, mitochondrial (Q9D6J5) [more info...]
Chain information for AF-Q9D6J5-ndufb8.pdb #18
---
Chain | Description | UniProt
A | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial |
NDUB8_MOUSE
> ui tool show Matchmaker
> matchmaker #7-9,11-18 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CI_pdb-6ZR2, chain P (#5) with AF-Q9DC69-ndufa9.pdb, chain A (#7),
sequence alignment score = 1614.6
RMSD between 339 pruned atom pairs is 0.626 angstroms; (across all 342 pairs:
0.669)
Matchmaker CI_pdb-6ZR2, chain B (#5) with AF-Q9DC70-ndufs7.pdb, chain A (#8),
sequence alignment score = 778.9
RMSD between 154 pruned atom pairs is 0.499 angstroms; (across all 156 pairs:
0.822)
Matchmaker CI_pdb-6ZR2, chain p (#5) with AF-Q9DCS9-ndufb10.pdb, chain A (#9),
sequence alignment score = 891.7
RMSD between 166 pruned atom pairs is 0.735 angstroms; (across all 169 pairs:
0.886)
Matchmaker CI_pdb-6ZR2, chain F (#5) with AF-Q91YT0-nudfv1.pdb, chain A (#11),
sequence alignment score = 2095.7
RMSD between 428 pruned atom pairs is 0.565 angstroms; (across all 428 pairs:
0.565)
Matchmaker CI_pdb-6ZR2, chain s (#5) with AF-Q8BK30-ndufv3.pdb, chain A (#12),
sequence alignment score = 207.7
RMSD between 41 pruned atom pairs is 0.611 angstroms; (across all 41 pairs:
0.611)
Matchmaker CI_pdb-6ZR2, chain S (#5) with AF-Q9CQ75-ndufa2.pdb, chain A (#13),
sequence alignment score = 389.4
RMSD between 82 pruned atom pairs is 0.491 angstroms; (across all 83 pairs:
0.613)
Matchmaker CI_pdb-6ZR2, chain m (#5) with AF-Q9CQC7-ndufb4.pdb, chain A (#14),
sequence alignment score = 627.3
RMSD between 116 pruned atom pairs is 1.074 angstroms; (across all 126 pairs:
1.337)
Matchmaker CI_pdb-6ZR2, chain h (#5) with AF-Q9CQH3-ndufb5.pdb, chain A (#15),
sequence alignment score = 695.3
RMSD between 125 pruned atom pairs is 0.867 angstroms; (across all 138 pairs:
1.168)
Matchmaker CI_pdb-6ZR2, chain k (#5) with AF-Q9CQZ6-ndufb3.pdb, chain A (#16),
sequence alignment score = 361.1
RMSD between 74 pruned atom pairs is 0.725 angstroms; (across all 75 pairs:
0.772)
Matchmaker CI_pdb-6ZR2, chain U (#5) with AF-Q9CR21-ndufab1.pdb, chain A
(#17), sequence alignment score = 431.4
RMSD between 82 pruned atom pairs is 0.571 angstroms; (across all 86 pairs:
0.805)
Matchmaker CI_pdb-6ZR2, chain l (#5) with AF-Q9D6J5-ndufb8.pdb, chain A (#18),
sequence alignment score = 795
RMSD between 147 pruned atom pairs is 0.786 angstroms; (across all 154 pairs:
0.939)
> show #!5 models
> color #5 #8d8d8d19
> transparency #5 0 target c
> transparency #5 0.9 target c
> transparency #5 0.9 target cs
> transparency #5 0.9 target csa
> transparency #5 0.99 target csa
> hide #!5 models
> hide #9:1-35 target c
> hide #7:1-35 target c
> hide #8:1-36 target c
> hide #12:1-35 target c
> hide #15:1-46 target c
> select #15
1534 atoms, 1576 bonds, 189 residues, 1 model selected
> ~select #15
Nothing selected
> select #15
1534 atoms, 1576 bonds, 189 residues, 1 model selected
> ~select #15
Nothing selected
> hide #17:1-68 target c
> hide #18:1-29 target c
> show #!5 models
> hide #11:1-20 target c
> show #!2 models
> select #2/A,K
3956 atoms, 4040 bonds, 499 residues, 1 model selected
> hide #!5 models
> hide #18 models
> hide #17 models
> hide #16 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> select #2/A,K
3956 atoms, 4040 bonds, 499 residues, 1 model selected
> select #2/A, K
3956 atoms, 4040 bonds, 499 residues, 1 model selected
> select #2\K
Expected an objects specifier or a keyword
> select #2/L
3483 atoms, 3552 bonds, 446 residues, 1 model selected
> select #2/T
554 atoms, 565 bonds, 78 residues, 1 model selected
> select clear
> select #2/A-H,J,K,T
17157 atoms, 17565 bonds, 20 pseudobonds, 2134 residues, 2 models selected
> select clear
> select #2/A-H,J,K,T
17157 atoms, 17565 bonds, 20 pseudobonds, 2134 residues, 2 models selected
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/cIII_mon1.pdb
> selectedOnly true
> hide #9 models
> hide #8 models
> hide #7 models
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/cIII_mon1.pdb
Chain information for cIII_mon1.pdb #19
---
Chain | Description
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
J | No description available
K | No description available
T | No description available
> hide sel atoms
> select clear
> hide #!2,19 atoms
> show #!2,19 cartoons
> select #2/L-S, U,V
16543 atoms, 16940 bonds, 23 pseudobonds, 2051 residues, 2 models selected
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/cIII_mon2.pdb
> selectedOnly true
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/cIII_mon2.pdb
Summary of feedback from opening
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/cIII_mon2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 71
ASP A 74 1 4
Start residue of secondary structure not found: HELIX 2 2 THR A 79 LEU A 85 1
7
Start residue of secondary structure not found: HELIX 3 3 ASP A 86 PHE A 90 1
5
Start residue of secondary structure not found: HELIX 4 4 PRO B 28 SER B 30 1
3
Start residue of secondary structure not found: HELIX 5 5 GLN B 31 TYR B 41 1
11
111 messages similar to the above omitted
End residue of secondary structure not found: HELIX 117 117 CYS L 35 GLN L 37
1 3
Start residue of secondary structure not found: HELIX 118 118 GLU L 39 SER L
56 1 18
Start residue of secondary structure not found: HELIX 119 119 THR L 66 CYS L
79 1 14
Start residue of secondary structure not found: HELIX 120 120 VAL L 80 HIS L
82 1 3
Start residue of secondary structure not found: HELIX 121 121 LEU L 84 ASN L
87 1 4
Start residue of secondary structure not found: HELIX 122 122 ILE M 6 PHE M 15
1 10
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 139 139 SER N 205 VAL N
208 1 4
Start residue of secondary structure not found: HELIX 140 140 ARG N 213 HIS N
223 1 11
Start residue of secondary structure not found: HELIX 141 141 ALA N 226 ARG N
228 1 3
Start residue of secondary structure not found: HELIX 142 142 HIS N 239 LEU N
250 1 12
Start residue of secondary structure not found: HELIX 143 143 PRO N 299 ASN N
301 1 3
Start residue of secondary structure not found: HELIX 144 144 VAL N 302 ILE N
311 1 10
55 messages similar to the above omitted
End residue of secondary structure not found: HELIX 200 200 ASP S 39 GLN S 42
1 4
Start residue of secondary structure not found: HELIX 201 201 GLY S 45 ALA S
53 1 9
Start residue of secondary structure not found: HELIX 202 202 ALA S 54 LYS S
56 1 3
Start residue of secondary structure not found: HELIX 203 203 ALA T 3 ARG T 5
1 3
Start residue of secondary structure not found: HELIX 204 204 ALA T 6 SER T 8
1 3
Start residue of secondary structure not found: HELIX 205 205 SER T 30 ASP T
32 1 3
13 messages similar to the above omitted
End residue of secondary structure not found: HELIX 219 219 LEU V 2 GLN V 13 1
12
Start residue of secondary structure not found: HELIX 220 220 VAL V 28 GLN V
36 1 9
Start residue of secondary structure not found: HELIX 221 221 VAL V 43 LEU V
45 1 3
Start residue of secondary structure not found: HELIX 222 222 ALA V 49 ALA V
77 1 29
Start residue of secondary structure not found: HELIX 223 223 ALA W 2 ASN W 11
1 10
Start residue of secondary structure not found: HELIX 224 224 THR W 27 ALA W
46 1 20
59 messages similar to the above omitted
Chain information for cIII_mon2.pdb #20
---
Chain | Description
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
U | No description available
V | No description available
> select clear
> hide #!2,19-20 cartoons
> show #!2,19-20 cartoons
> hide #!2,19-20 atoms
> show #!2,19-20 cartoons
> hide #!2 models
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q9CZ13-uqcrc1.pdb
AF-Q9CZ13-uqcrc1.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 1, mitochondrial
(Q9CZ13) [more info...]
Chain information for AF-Q9CZ13-uqcrc1.pdb #21
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 1, mitochondrial | QCR1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q9D855-uqcrb.pdb
AF-Q9D855-uqcrb.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 7 (Q9D855) [more
info...]
Chain information for AF-Q9D855-uqcrb.pdb #22
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 7 | QCR7_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q9DB77-uqcrc2.pdb
AF-Q9DB77-uqcrc2.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 2, mitochondrial
(Q9DB77) [more info...]
Chain information for AF-Q9DB77-uqcrc2.pdb #23
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 2, mitochondrial | QCR2_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-P99028-uqcrh.pdb
AF-P99028-uqcrh.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 6, mitochondrial
(P99028) [more info...]
Chain information for AF-P99028-uqcrh.pdb #24
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 6, mitochondrial | QCR6_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q8R1I1-uqcr10.pdb
AF-Q8R1I1-uqcr10.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 9 (Q8R1I1) [more
info...]
Chain information for AF-Q8R1I1-uqcr10.pdb #25
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 9 | QCR9_MOUSE
> ui tool show Matchmaker
> matchmaker #21-25 to #19
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker cIII_mon1.pdb, chain A (#19) with AF-Q9CZ13-uqcrc1.pdb, chain A
(#21), sequence alignment score = 2238.4
RMSD between 439 pruned atom pairs is 0.451 angstroms; (across all 446 pairs:
0.571)
Matchmaker cIII_mon1.pdb, chain F (#19) with AF-Q9D855-uqcrb.pdb, chain A
(#22), sequence alignment score = 520.3
RMSD between 101 pruned atom pairs is 0.553 angstroms; (across all 102 pairs:
0.615)
Matchmaker cIII_mon1.pdb, chain B (#19) with AF-Q9DB77-uqcrc2.pdb, chain A
(#23), sequence alignment score = 2031.8
RMSD between 410 pruned atom pairs is 0.680 angstroms; (across all 420 pairs:
0.860)
Matchmaker cIII_mon1.pdb, chain H (#19) with AF-P99028-uqcrh.pdb, chain A
(#24), sequence alignment score = 352.6
RMSD between 68 pruned atom pairs is 0.743 angstroms; (across all 68 pairs:
0.743)
Matchmaker cIII_mon1.pdb, chain J (#19) with AF-Q8R1I1-uqcr10.pdb, chain A
(#25), sequence alignment score = 309.3
RMSD between 60 pruned atom pairs is 0.458 angstroms; (across all 60 pairs:
0.458)
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q9CZ13-uqcrc1.pdb
AF-Q9CZ13-uqcrc1.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 1, mitochondrial
(Q9CZ13) [more info...]
Chain information for AF-Q9CZ13-uqcrc1.pdb #26
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 1, mitochondrial | QCR1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q9D855-uqcrb.pdb
AF-Q9D855-uqcrb.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 7 (Q9D855) [more
info...]
Chain information for AF-Q9D855-uqcrb.pdb #27
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 7 | QCR7_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q9DB77-uqcrc2.pdb
AF-Q9DB77-uqcrc2.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 2, mitochondrial
(Q9DB77) [more info...]
Chain information for AF-Q9DB77-uqcrc2.pdb #28
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 2, mitochondrial | QCR2_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-P99028-uqcrh.pdb
AF-P99028-uqcrh.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 6, mitochondrial
(P99028) [more info...]
Chain information for AF-P99028-uqcrh.pdb #29
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 6, mitochondrial | QCR6_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIII/AF-Q8R1I1-uqcr10.pdb
AF-Q8R1I1-uqcr10.pdb title:
Alphafold V2.0 prediction for cytochrome B-C1 complex subunit 9 (Q8R1I1) [more
info...]
Chain information for AF-Q8R1I1-uqcr10.pdb #30
---
Chain | Description | UniProt
A | cytochrome B-C1 complex subunit 9 | QCR9_MOUSE
> ui tool show Matchmaker
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #25 models
> ui tool show Matchmaker
> matchmaker #26-30 to #20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker cIII_mon2.pdb, chain L (#20) with AF-Q9CZ13-uqcrc1.pdb, chain A
(#26), sequence alignment score = 2190.5
RMSD between 439 pruned atom pairs is 0.444 angstroms; (across all 445 pairs:
0.554)
Matchmaker cIII_mon2.pdb, chain Q (#20) with AF-Q9D855-uqcrb.pdb, chain A
(#27), sequence alignment score = 510.3
RMSD between 101 pruned atom pairs is 0.552 angstroms; (across all 101 pairs:
0.552)
Matchmaker cIII_mon2.pdb, chain M (#20) with AF-Q9DB77-uqcrc2.pdb, chain A
(#28), sequence alignment score = 2042.6
RMSD between 404 pruned atom pairs is 0.599 angstroms; (across all 420 pairs:
0.842)
Matchmaker cIII_mon2.pdb, chain S (#20) with AF-P99028-uqcrh.pdb, chain A
(#29), sequence alignment score = 356.2
RMSD between 67 pruned atom pairs is 0.703 angstroms; (across all 68 pairs:
1.092)
Matchmaker cIII_mon2.pdb, chain U (#20) with AF-Q8R1I1-uqcr10.pdb, chain A
(#30), sequence alignment score = 312.9
RMSD between 59 pruned atom pairs is 0.529 angstroms; (across all 60 pairs:
0.592)
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> color #2 #00000019
> color #2 #00550019
> transparency 0 target c
> hide #!19 models
> hide #!20 models
> color #3 #ff550019
> transparency #3 0 target c
> transparency #4 0 target c
> color #4 #ffaa00 transparency 0
> color #5 #0055ff transparency 0
> save
> C:\Users\Hevle001\Desktop\Respirasome_manuscript\respirasome_final_structure
> width 2400 height 2400 transparentBackground true
Cannot determine format for
'C:\Users\Hevle001\Desktop\Respirasome_manuscript\respirasome_final_structure'
> save
> C:\Users\Hevle001\Desktop\Respirasome_manuscript\respirasome_final_structure.png
> width 2400 height 2400 transparentBackground true
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #30 models
> show #29 models
> show #28 models
> show #27 models
> show #26 models
> show #22 models
> show #21 models
> show #23 models
> show #24 models
> show #25 models
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/respirasome_for_images_w_xlinks.cxs
——— End of log from Mon Feb 28 12:28:37 2022 ———
opened ChimeraX session
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P19536-cox5b.pdb
AF-P19536-cox5b.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 5B, mitochondrial
(P19536) [more info...]
Chain information for AF-P19536-cox5b.pdb #31
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 5B, mitochondrial | COX5B_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P19783-cox4i1.pdb
AF-P19783-cox4i1.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 4 isoform 1,
mitochondrial (P19783) [more info...]
Chain information for AF-P19783-cox4i1.pdb #32
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P43024-cox6a1.pdb
AF-P43024-cox6a1.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 6A1, mitochondrial
(P43024) [more info...]
Chain information for AF-P43024-cox6a1.pdb #33
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 6A1, mitochondrial | CX6A1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P48771-cox7a2.pdb
AF-P48771-cox7a2.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 7A2, mitochondrial
(P48771) [more info...]
Chain information for AF-P48771-cox7a2.pdb #34
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 7A2, mitochondrial | CX7A2_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P56391-cox6b1.pdb
AF-P56391-cox6b1.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 6B1 (P56391) [more
info...]
Chain information for AF-P56391-cox6b1.pdb #35
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 6B1 | CX6B1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-Q9CPQ1-cox6c.pdb
AF-Q9CPQ1-cox6c.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 6C (Q9CPQ1) [more
info...]
Chain information for AF-Q9CPQ1-cox6c.pdb #36
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 6C | COX6C_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P12787-cox5a.pdb
AF-P12787-cox5a.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 5A, mitochondrial
(P12787) [more info...]
Chain information for AF-P12787-cox5a.pdb #37
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 5A, mitochondrial | COX5A_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P17665-cox7c.pdb
AF-P17665-cox7c.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 7C, mitochondrial
(P17665) [more info...]
Chain information for AF-P17665-cox7c.pdb #38
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 7C, mitochondrial | COX7C_MOUSE
> select clear
> ui tool show Matchmaker
> matchmaker #31-38 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CIV_pdb-7O3E, chain f (#3) with AF-P19536-cox5b.pdb, chain A (#31),
sequence alignment score = 499.5
RMSD between 87 pruned atom pairs is 0.718 angstroms; (across all 95 pairs:
1.903)
Matchmaker CIV_pdb-7O3E, chain d (#3) with AF-P19783-cox4i1.pdb, chain A
(#32), sequence alignment score = 747.4
RMSD between 138 pruned atom pairs is 0.814 angstroms; (across all 144 pairs:
1.621)
Matchmaker CIV_pdb-7O3E, chain g (#3) with AF-P43024-cox6a1.pdb, chain A
(#33), sequence alignment score = 285.2
RMSD between 68 pruned atom pairs is 0.956 angstroms; (across all 74 pairs:
1.890)
Matchmaker CIV_pdb-7O3E, chain I (#3) with AF-P48771-cox7a2.pdb, chain A
(#34), sequence alignment score = 194.8
RMSD between 53 pruned atom pairs is 0.711 angstroms; (across all 67 pairs:
15.426)
Matchmaker CIV_pdb-7O3E, chain h (#3) with AF-P56391-cox6b1.pdb, chain A
(#35), sequence alignment score = 437.5
RMSD between 70 pruned atom pairs is 0.797 angstroms; (across all 79 pairs:
3.053)
Matchmaker CIV_pdb-7O3E, chain i (#3) with AF-Q9CPQ1-cox6c.pdb, chain A (#36),
sequence alignment score = 373.6
RMSD between 57 pruned atom pairs is 0.939 angstroms; (across all 72 pairs:
1.704)
Matchmaker CIV_pdb-7O3E, chain e (#3) with AF-P12787-cox5a.pdb, chain A (#37),
sequence alignment score = 547.8
RMSD between 104 pruned atom pairs is 0.572 angstroms; (across all 104 pairs:
0.572)
Matchmaker CIV_pdb-7O3E, chain l (#3) with AF-P17665-cox7c.pdb, chain A (#38),
sequence alignment score = 242.5
RMSD between 45 pruned atom pairs is 0.432 angstroms; (across all 46 pairs:
0.592)
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P43024-cox6a1.pdb
AF-P43024-cox6a1.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 6A1, mitochondrial
(P43024) [more info...]
Chain information for AF-P43024-cox6a1.pdb #39
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 6A1, mitochondrial | CX6A1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P48771-cox7a2.pdb
AF-P48771-cox7a2.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 7A2, mitochondrial
(P48771) [more info...]
Chain information for AF-P48771-cox7a2.pdb #40
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 7A2, mitochondrial | CX7A2_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P56391-cox6b1.pdb
AF-P56391-cox6b1.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 6B1 (P56391) [more
info...]
Chain information for AF-P56391-cox6b1.pdb #41
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 6B1 | CX6B1_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-Q9CPQ1-cox6c.pdb
AF-Q9CPQ1-cox6c.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 6C (Q9CPQ1) [more
info...]
Chain information for AF-Q9CPQ1-cox6c.pdb #42
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 6C | COX6C_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P12787-cox5a.pdb
AF-P12787-cox5a.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 5A, mitochondrial
(P12787) [more info...]
Chain information for AF-P12787-cox5a.pdb #43
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 5A, mitochondrial | COX5A_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P17665-cox7c.pdb
AF-P17665-cox7c.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 7C, mitochondrial
(P17665) [more info...]
Chain information for AF-P17665-cox7c.pdb #44
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 7C, mitochondrial | COX7C_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P19536-cox5b.pdb
AF-P19536-cox5b.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 5B, mitochondrial
(P19536) [more info...]
Chain information for AF-P19536-cox5b.pdb #45
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 5B, mitochondrial | COX5B_MOUSE
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/chimera_sessions/AF_models_xlinked_subunits/complexIV/AF-P19783-cox4i1.pdb
AF-P19783-cox4i1.pdb title:
Alphafold V2.0 prediction for cytochrome C oxidase subunit 4 isoform 1,
mitochondrial (P19783) [more info...]
Chain information for AF-P19783-cox4i1.pdb #46
---
Chain | Description | UniProt
A | cytochrome C oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE
> ui tool show Matchmaker
> matchmaker #39-46 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CIV-alt_pdb-7O3E, chain g (#4) with AF-P43024-cox6a1.pdb, chain A
(#39), sequence alignment score = 285.2
RMSD between 68 pruned atom pairs is 0.956 angstroms; (across all 74 pairs:
1.890)
Matchmaker CIV-alt_pdb-7O3E, chain I (#4) with AF-P48771-cox7a2.pdb, chain A
(#40), sequence alignment score = 194.8
RMSD between 53 pruned atom pairs is 0.711 angstroms; (across all 67 pairs:
15.426)
Matchmaker CIV-alt_pdb-7O3E, chain h (#4) with AF-P56391-cox6b1.pdb, chain A
(#41), sequence alignment score = 437.5
RMSD between 70 pruned atom pairs is 0.797 angstroms; (across all 79 pairs:
3.053)
Matchmaker CIV-alt_pdb-7O3E, chain i (#4) with AF-Q9CPQ1-cox6c.pdb, chain A
(#42), sequence alignment score = 373.6
RMSD between 57 pruned atom pairs is 0.939 angstroms; (across all 72 pairs:
1.704)
Matchmaker CIV-alt_pdb-7O3E, chain e (#4) with AF-P12787-cox5a.pdb, chain A
(#43), sequence alignment score = 547.8
RMSD between 104 pruned atom pairs is 0.572 angstroms; (across all 104 pairs:
0.572)
Matchmaker CIV-alt_pdb-7O3E, chain l (#4) with AF-P17665-cox7c.pdb, chain A
(#44), sequence alignment score = 242.5
RMSD between 45 pruned atom pairs is 0.432 angstroms; (across all 46 pairs:
0.592)
Matchmaker CIV-alt_pdb-7O3E, chain f (#4) with AF-P19536-cox5b.pdb, chain A
(#45), sequence alignment score = 499.5
RMSD between 87 pruned atom pairs is 0.718 angstroms; (across all 95 pairs:
1.903)
Matchmaker CIV-alt_pdb-7O3E, chain d (#4) with AF-P19783-cox4i1.pdb, chain A
(#46), sequence alignment score = 747.4
RMSD between 138 pruned atom pairs is 0.814 angstroms; (across all 144 pairs:
1.621)
> hide #37,43:1-37 target c
> hide #38,44:1-316 target c
> hide #38,44:1-16 target c
> hide #31,45:1-30 target c
> hide #32,46:1-22 target c
> hide #24,29:1-13 target c
> hide #21,26:1-34 target c
> hide #23,28:1-14 target c
> show #13 models
> hide #13 models
> show #16 models
> hide #16 models
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/xlinked_subunits_w_alternative_cox_respirasome.cxs
> show #7 models
> show #8 models
> show #9 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #18 models
> color #5 #d95f02 transparency 0
> color #4 #1b9e77 transparency 0
> color #3 #1b9e77 transparency 0
> color #2 #7570b3 transparency 0
> color #21 #7570b3 transparency 0
> color #21-30 #7570b3 target c
> color #31-46 #1b9e77 target c
> color #7-9,11-18 #d95f02 target c
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #33,39:1-26 target c
> save
> C:\Users\Hevle001\Desktop\Respirasome_manuscript\respirasome_final_structure.png
> width 2400 height 2400 transparentBackground true
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/xlinked_subunits_w_alternative_cox_respirasome.cxs
——— End of log from Mon Feb 28 13:21:05 2022 ———
opened ChimeraX session
> ui tool show XMAS
Peptide pair mapping of PD evidence file:
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome.xlsx
Unique peptide pairs: 30 out of 30
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 5 time(s)]Unique peptide pairs with pseudobonds: 24
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 55 time(s)]Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.pb
Mapping information is stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.tsv
Peptide pair mapping of PD evidence file:
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/wt_inter_xl_respirasome.xlsx
Unique peptide pairs: 37 out of 37
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 5 time(s)]Unique peptide pairs with pseudobonds: 31
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 73 time(s)]Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/wt_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.pb
Mapping information is stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/wt_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.tsv
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:693: UserWarning: Tight layout not applied. The
left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
[Repeated 1 time(s)]Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_to55.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_from55.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_to55.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_from55.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
Traceback (most recent call last):
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 175, in <lambda>
self.is_selection_empty(f))
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 1356, in is_selection_empty
function(selection)
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 250, in show_visualize_dialog
custom_layout, reset_values = self.create_custom_layout(pbs)
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 400, in create_custom_layout
functions[j](widget, attribute, row_name,
File "C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 329, in color_button_function
color = group.single_color
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'PseudobondGroup' object has no attribute 'single_color'
AttributeError: 'PseudobondGroup' object has no attribute 'single_color'
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:693: UserWarning: Tight layout not applied. The
left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
> hide #47 models
> hide #48 models
> hide #49 models
> hide #50 models
> hide #52 models
> hide #54 models
> transparency 0.5 taget c
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 0.5 target c
> crosslinks 51,53 radius 1.5 dashes 0
Missing or invalid "pbonds" argument: invalid pseudobonds specifier
> crosslinks 51,53 radius 1.5
Missing or invalid "pbonds" argument: invalid pseudobonds specifier
> crosslinks #51,53 radius 1.5 dashes 0
> hide #53 models
> color #51 black models transparency 0
> show #52 models
> color #52 #aa0000 models transparency 0
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_to60.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_to60.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
> hide #52 models
> hide #51 models
> crosslinks #55,56 radius 1 dashes 0
> color #55 black models transparency 0
> color #56 black models transparency 0
> hide #56 models
> show #56 models
> hide #55 models
> show #55 models
> hide #55 models
> hide #56 models
> show #56 models
> show #55 models
> close 47-56
Expected a models specifier or a keyword
> close #47-56
Peptide pair mapping of PD evidence file:
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome.xlsx
Unique peptide pairs: 30 out of 30
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 5 time(s)]Unique peptide pairs with pseudobonds: 24
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 55 time(s)]Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.pb
Mapping information is stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.tsv
Distances updated in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/ki_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.tsv
> close #49
> close #48
> select clear
> hide #47 models
Peptide pair mapping of PD evidence file:
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/wt_inter_xl_respirasome.xlsx
Unique peptide pairs: 37 out of 37
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 5 time(s)]Unique peptide pairs with pseudobonds: 31
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\info_file.py:30: FutureWarning: The frame.append method
is deprecated and will be removed from pandas in a future version. Use
pandas.concat instead.
self.df = self.df.append(df_add, ignore_index=True)
[Repeated 73 time(s)]Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/wt_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.pb
Mapping information is stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Mapping_xlinks/new_mapping/wt_inter_xl_respirasome_7,8,9,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46.tsv
> hide #49 models
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:693: UserWarning: Tight layout not applied. The
left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_to60.pb
> hide #50 models
> hide #48 models
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_to60.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
> select clear
> close #52
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_to60.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:693: UserWarning: Tight layout not applied. The
left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_from60.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_from60.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\matplotlib_venn\\_venn3.py:117: UserWarning: Bad circle positioning
warnings.warn("Bad circle positioning")
> select clear
> hide #51 models
> hide #52 models
> hide #53 models
> hide #54 models
> show #53 models
> show #54 models
> select #5/T
648 atoms, 657 bonds, 77 residues, 1 model selected
> select #5/U
729 atoms, 741 bonds, 87 residues, 1 model selected
> mmaker
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> mmaker #17 to #5/T
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CI_pdb-6ZR2, chain T (#5) with AF-Q9CR21-ndufab1.pdb, chain A
(#17), sequence alignment score = 352.8
RMSD between 76 pruned atom pairs is 0.764 angstroms; (across all 76 pairs:
0.764)
> select clear
> close 51-54
Expected a models specifier or a keyword
> close #51-54
> close #48, 50
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:693: UserWarning: Tight layout not applied. The
left and right margins cannot be made large enough to accommodate all axes
decorations.
plt.tight_layout()
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_to60.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_to60.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py:703: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be
removed two minor releases later. Use manager.set_window_title or GUI-specific
methods instead.
figure.canvas.set_window_title(title)
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_to55.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_to55.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/wt_resp_from55.pb
Pseudobonds are stored in
C:/Users/Hevle001/Desktop/Respirasome_manuscript/ki_resp_from55.pb
C:\Users\Hevle001\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\matplotlib_venn\\_venn3.py:117: UserWarning: Bad circle positioning
warnings.warn("Bad circle positioning")
> hide #51 models
> hide #52 models
> hide #50 models
> crosslinks #53-56 radius 1 dashes 0
> crosslinks #53-54 color black
> crosslinks #55-56 color red
> hide #54 models
> hide #53 models
> show #53 models
> hide #55 models
> hide #56 models
> show #55 models
> hide #48 models
> hide #34,40:1-23 target c
> save
> C:\Users\Hevle001\Desktop\Respirasome_manuscript\respirasome_xlinks_wt.png
> width 2400 height 2400 transparentBackground true
> show #56 models
> hide #55 models
> show #54 models
> hide #53 models
> save
> C:\Users\Hevle001\Desktop\Respirasome_manuscript\respirasome_xlinks_ki.png
> width 2400 height 2400 transparentBackground true
> hide #56 models
> show #56 models
> show #52 models
> hide #52 models
> show #52 models
> hide #52 models
> hide #54 models
> hide #56 models
> show #51 models
> hide #51 models
> show #51 models
> show #52 models
> hide #52 models
> show #52 models
> hide #52 models
> show #52 models
> hide #51 models
> hide #52 models
> show #52 models
> crosslinks #51, 52 radius 1 dashes 0
> crosslinks #51, 52 color black
> hide #52 models
> show #51 models
> show #52 models
> hide #51 models
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/alternative_cox_position.cxs
——— End of log from Tue Mar 1 16:31:55 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\dist_monitor\monitor.py", line 104, in _changes_handler
pbg = pb.group
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
Error processing trigger "changes":
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> hide all
> hide #7 models
> hide #8 models
> hide #9 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #25 models
> hide #26 models
> hide #27 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #31 models
> hide #32 models
> hide #33 models
> hide #34 models
> hide #35 models
> hide #36 models
> hide #37 models
> hide #38 models
> hide #39 models
> hide #40 models
> hide #41 models
> hide #42 models
> hide #43 models
> hide #44 models
> hide #45 models
> hide #46 models
> hide #52 models
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/interface_analysis_respirasome/modified_structures/7O3E_COX_mod_w_cox7a2.pdb
Chain information for 7O3E_COX_mod_w_cox7a2.pdb #57
---
Chain | Description
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
a | No description available
b | No description available
c | No description available
k | No description available
m | No description available
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/interface_analysis_respirasome/modified_structures/7O3H_mod.pdb
Chain information for 7O3H_mod.pdb #58
---
Chain | Description
A B | No description available
C N | No description available
D | No description available
E P | No description available
F H | No description available
G | No description available
I J | No description available
K | No description available
L M | No description available
O | No description available
Q S | No description available
R | No description available
T | No description available
V | No description available
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/interface_analysis_respirasome/modified_structures/6ZR2_mod.pdb
Chain information for 6ZR2_mod.pdb #59
---
Chain | Description
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
> open
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/interface_analysis_respirasome/modified_structures/7O3E_COX_mod_w_cox7a2.pdb
Chain information for 7O3E_COX_mod_w_cox7a2.pdb #60
---
Chain | Description
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
a | No description available
b | No description available
c | No description available
k | No description available
m | No description available
> hide #!2-5,57-60 atoms
> show #!2-5,57-60 cartoons
> mmaker #59 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CI_pdb-6ZR2, chain G (#5) with 6ZR2_mod.pdb, chain G (#59),
sequence alignment score = 3480.6
RMSD between 688 pruned atom pairs is 0.000 angstroms; (across all 688 pairs:
0.000)
> mmaker #57 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CIV_pdb-7O3E, chain a (#3) with 7O3E_COX_mod_w_cox7a2.pdb, chain a
(#57), sequence alignment score = 2750.3
RMSD between 514 pruned atom pairs is 0.000 angstroms; (across all 514 pairs:
0.000)
> mmaker #60 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CIV-alt_pdb-7O3E, chain a (#4) with 7O3E_COX_mod_w_cox7a2.pdb,
chain a (#60), sequence alignment score = 2750.3
RMSD between 514 pruned atom pairs is 0.000 angstroms; (across all 514 pairs:
0.000)
> mmaker #58 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CIII2_pdb-7O3H, chain A (#2) with 7O3H_mod.pdb, chain I (#58),
sequence alignment score = 2239
RMSD between 439 pruned atom pairs is 0.451 angstroms; (across all 446 pairs:
0.571)
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #57
14833 atoms, 15274 bonds, 29 pseudobonds, 1835 residues, 2 models selected
> select #58
34143 atoms, 34955 bonds, 43 pseudobonds, 4263 residues, 2 models selected
> select #59
66807 atoms, 68499 bonds, 30 pseudobonds, 8232 residues, 3 models selected
> select #57-60
130616 atoms, 134002 bonds, 131 pseudobonds, 16165 residues, 9 models selected
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/Respirasome_w_alt_COX_af_subunits.cxs
Exception ignored in: <function Drawing.__del__ at 0x0000027ECD0CBAF0>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1183, in __del__
if not self.was_deleted:
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted'
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 250, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 250, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2365, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 49, in python_instances_of_class
return [x for x in instances if filt(x)]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 49, in <listcomp>
return [x for x in instances if filt(x)]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 44, in <lambda>
filt = lambda x: (not x.group.structure) or x.group.structure.id
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\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 1.3\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 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\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 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 250, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 250, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2365, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 49, in python_instances_of_class
return [x for x in instances if filt(x)]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 49, in <listcomp>
return [x for x in instances if filt(x)]
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 44, in <lambda>
filt = lambda x: (not x.group.structure) or x.group.structure.id
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> select clear
> close #1-56
> select #57-60
130616 atoms, 134002 bonds, 131 pseudobonds, 16165 residues, 9 models selected
> save
> C:/Users/Hevle001/Desktop/Respirasome_manuscript/structural_analysis/resp_mod_alt_cox_af_subunits.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\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 1.3\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 1.3\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\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 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 619, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 30.0.101.1191
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 10 Enterprise (Build 19043)
Memory: 34,131,087,360
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900 CPU @ 3.10GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-XMAS: 1.0.1
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
et-xmlfile: 1.1.0
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
matplotlib-venn: 0.11.6
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openpyxl: 3.0.9
openvr: 1.16.801
packaging: 21.3
pandas: 1.4.0
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
seaborn: 0.11.2
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Bad pseudobond / group attributes |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Would need the alternative_cox_position.cxs session file to have any ability to investigate.