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Opened 5 years ago
Closed 5 years ago
#3839 closed defect (duplicate)
KeyError deleting models during 'close session'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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: Linux-5.4.0-51-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202009290239 (2020-09-29 02:39:03 UTC)
Description
Attempt to close my session.
Log:
UCSF ChimeraX version: 1.2.dev202009290239 (2020-09-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> format session
Log from Fri Oct 16 15:55:11 2020UCSF ChimeraX version: 1.2.dev202009290239
(2020-09-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> format session
Log from Fri Oct 16 15:41:51 2020UCSF ChimeraX version: 1.2.dev202009290239
(2020-09-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
Log from Fri Oct 16 15:07:29 2020UCSF ChimeraX version: 1.2.dev202009290239
(2020-09-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
Log from Thu Sep 17 14:46:41 2020 Startup Errors
---
error | Bundle 'ChimeraX-Registration' custom initialization failed
warning | Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 432, in initialize
api._api_caller.initialize(api, session, self)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1633, in initialize
return cls._get_func(api, "initialize")(session, bi)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize
nag(session)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag
if not check_registration(logger=session.logger):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration
return _check_expiration(param, logger)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 131, in _check_expiration
expires = datetime.strptime(param["Expires"], TimeFormat)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/_strptime.py", line 577, in
_strptime_datetime
tt, fraction, gmtoff_fraction = _strptime(data_string, format)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/_strptime.py", line 359, in
_strptime
(data_string, format))
ValueError: time data 'Tue Dec 8 23:48:19 2020' does not match format '%a %b
%d %H:%M:%S %Y'
UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: Service Unavailable
> open 2hvr
Summary of feedback from opening 2hvr fetched from pdb
---
warnings | Apparent non-polymeric linkage between A #236 and DC #237 in chain
E
Apparent non-polymeric linkage between A #236 and DC #237 in chain H
notes | Fetching compressed mmCIF 2hvr from
http://files.rcsb.org/download/2hvr.cif
Fetching CCD BTB from http://ligand-expo.rcsb.org/reports/B/BTB/BTB.cif
Fetching CCD O2C from http://ligand-expo.rcsb.org/reports/O/O2C/O2C.cif
2hvr title:
Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex
containing a 3'-deoxyribonucleotide at the nick [more info...]
Chain information for 2hvr #1
---
Chain | Description
A B | T4 RNA ligase 2
C F |
5'-D(*ap*TP*TP*CP*CP*GP*ap*TP*ap*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*ap*ap*TP*TP*G)-3'
D G | 5'-D(*CP*ap*ap*TP*TP*GP*CP*GP*ap*C)-R(P*(omc)P*C)-3'
E H | 5'-R(P*A)-D(P*CP*ap*CP*TP*ap*TP*CP*GP*GP*ap*ap*T)-3'
Non-standard residues in 2hvr #1
---
BTB — 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol (bis-
tris buffer)
2hvr mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open 2hvq
Summary of feedback from opening 2hvq fetched from pdb
---
notes | Fetching compressed mmCIF 2hvq from
http://files.rcsb.org/download/2hvq.cif
Fetching CCD APK from http://ligand-expo.rcsb.org/reports/A/APK/APK.cif
2hvq title:
Structure of Adenylated full-length T4 RNA Ligase 2 [more info...]
Chain information for 2hvq #2
---
Chain | Description
A | Hypothetical 37.6 kDa protein in Gp24-hoc intergenic region
Non-standard residues in 2hvq #2
---
MG — magnesium ion
> show cartoons
> hide atoms
> hide #!1 models
> show #!1 models
> select #1/G:131
19 atoms, 20 bonds, 1 model selected
> select up
1097 atoms, 1218 bonds, 1 model selected
> select up
3584 atoms, 3706 bonds, 1 model selected
> delete sel
> hide #!2 models
> show #!2 models
> matchmaker #2 on #1
Expected a keyword
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hvr, chain A (#1) with 2hvq, chain A (#2), sequence alignment
score = 1641.9
RMSD between 225 pruned atom pairs is 0.512 angstroms; (across all 312 pairs:
33.056)
> matchmaker #2:244-328 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hvr, chain A (#1) with 2hvq, chain A (#2), sequence alignment
score = 389.6
RMSD between 76 pruned atom pairs is 0.957 angstroms; (across all 80 pairs:
1.192)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hvr, chain A (#1) with 2hvq, chain A (#2), sequence alignment
score = 1641.9
RMSD between 225 pruned atom pairs is 0.512 angstroms; (across all 312 pairs:
33.056)
> select #1/E:237
20 atoms, 21 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select clear
> select #1/D:136
19 atoms, 20 bonds, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 19 atom styles
> set bgColor white
> graphics silhouettes true
> lighting simple
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/A:172
7 atoms, 6 bonds, 1 model selected
> select up
87 atoms, 89 bonds, 1 model selected
> select up
2637 atoms, 2569 bonds, 1 model selected
Alignment identifier is 2.A
> select clear
> show sel atoms
> select clear
> show #!1 models
> select #1/A:35
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> select #1/D:136
19 atoms, 20 bonds, 1 model selected
> hide sel cartoons
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 81 atom styles
> hide #!2 models
> color sel byhetero
> select clear
> select #1/A:231
5 atoms, 4 bonds, 1 model selected
> select #1/E:239
19 atoms, 20 bonds, 1 model selected
> select up
268 atoms, 300 bonds, 1 model selected
Alignment identifier is 1.E
> select clear
> select #1/E:243
19 atoms, 20 bonds, 1 model selected
> select up
268 atoms, 300 bonds, 1 model selected
> select up
3635 atoms, 3719 bonds, 1 model selected
> select down
268 atoms, 300 bonds, 1 model selected
> select clear
> select #1/E
268 atoms, 300 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 268 atom styles
> color sel byhetero
> select clear
> hide sel atoms
> select clear
> show sel atoms
> select clear
> show #!2 models
> open 2hvs
Summary of feedback from opening 2hvs fetched from pdb
---
notes | Fetching compressed mmCIF 2hvs from
http://files.rcsb.org/download/2hvs.cif
Fetching CCD AMP from http://ligand-expo.rcsb.org/reports/A/AMP/AMP.cif
2hvs title:
Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex
containing a 2'-deoxyribonucleotide at the nick [more info...]
Chain information for 2hvs #3
---
Chain | Description
A B | T4 RNA Ligase 2
C F |
5'-D(*ap*TP*TP*CP*CP*GP*ap*TP*ap*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*ap*ap*TP*TP*G)-3'
D G | 5'-D(*CP*ap*ap*TP*TP*GP*CP*GP*ap*C)-R(P*(omc)P*C)-3'
E H | 5'-D(P*CP*ap*CP*TP*ap*TP*CP*GP*GP*ap*ap*T)-3'
Non-standard residues in 2hvs #3
---
AMP — adenosine monophosphate
BTB — 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol (bis-
tris buffer)
2hvs mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hvr, chain A (#1) with 2hvs, chain A (#3), sequence alignment
score = 1691.7
RMSD between 319 pruned atom pairs is 0.421 angstroms; (across all 319 pairs:
0.421)
> select #3
7188 atoms, 7425 bonds, 94 pseudobonds, 3 models selected
> show sel cartoons
> hide sel atoms
> hide #!2 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/B:136
12 atoms, 12 bonds, 1 model selected
> select up
1063 atoms, 1181 bonds, 1 model selected
> select up
3575 atoms, 3706 bonds, 1 model selected
> delete sel
> hide #!1 models
> select #3/E:237
19 atoms, 20 bonds, 1 model selected
> select up
245 atoms, 274 bonds, 1 model selected
> select up
269 atoms, 300 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 269 atom styles
> color sel byhetero
> select clear
> select #3/E:238
21 atoms, 23 bonds, 1 model selected
> select up
245 atoms, 274 bonds, 1 model selected
> select up
269 atoms, 300 bonds, 1 model selected
Alignment identifier is 3.E
> select clear
> hide sel atoms
> select clear
> select clear
> select #3/E:237
19 atoms, 20 bonds, 1 model selected
> hide sel cartoons
> select #3/D:136
19 atoms, 20 bonds, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 19 atom styles
> color sel byhetero
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 40 atom styles
> color sel byhetero
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select clear
> select #3/A:35
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> toolshed show "Side View"
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> select #1/E:236@C3'
1 atom, 1 model selected
> select up
22 atoms, 24 bonds, 1 model selected
> select up
268 atoms, 300 bonds, 1 model selected
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select up
2 atoms, 1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select #2/A:35@N6
1 atom, 1 model selected
> select up
31 atoms, 33 bonds, 1 model selected
> contacts restrict #2
43980 contacts
> close #4
> contacts sel restrict #2
61 contacts
> contacts sel restrict #2 reveal true
61 contacts
> select clear
> select up
2 atoms, 1 bond, 1 model selected
> select up
31 atoms, 33 bonds, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #2/A:33
11 atoms, 10 bonds, 1 model selected
> select up
55 atoms, 56 bonds, 1 model selected
> select up
2637 atoms, 2569 bonds, 1 model selected
> color sel byhetero
> select clear
> save2 "/home/ondragahura/Work/Lab Book/RNA_ligases_HMC/RNA_lig.cxs"
> open 5cot
Summary of feedback from opening 5cot fetched from pdb
---
note | Fetching compressed mmCIF 5cot from
http://files.rcsb.org/download/5cot.cif
5cot title:
Structure and mechanism of a eukaryal nick-sealing RNA ligase [more info...]
Chain information for 5cot #4
---
Chain | Description
A | Naegleria gruberi RNA ligase
Non-standard residues in 5cot #4
---
AMP — adenosine monophosphate
UNX — unknown atom or ion
> matchmaker #5 to #1
No molecules/chains to match specified
> matchmaker #5 to #1/A
No molecules/chains to match specified
> matchmaker #4 to #1/A
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 2hvr, chain A (#1) with 5cot, chain A (#4), sequence alignment
score = 175.1
RMSD between 73 pruned atom pairs is 0.804 angstroms; (across all 193 pairs:
8.703)
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> select #4/A:401@C5'
1 atom, 1 model selected
> select up
22 atoms, 24 bonds, 1 model selected
> select up
3264 atoms, 2789 bonds, 1 model selected
> select down
22 atoms, 24 bonds, 1 model selected
> color sel magenta
> color sel byhetero
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #4 models
> select #2/A:209
9 atoms, 8 bonds, 1 model selected
> select #2/A:207
7 atoms, 6 bonds, 1 model selected
> hide HOH
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select HOH
Expected an objects specifier or a keyword
> select clear
> select ::name="HOH"
784 atoms, 4 models selected
> hide sel
> select clear
> show #4 models
> open2 "/home/ondragahura/Work/Lab
> Book/RNA_ligases_HMC/Modes/EcRnl2_Phyre_1s68a.pdb"
> /home/ondragahura/Work/Lab
> Book/RNA_ligases_HMC/Modes/EcRnl2_SwissModel_6vt4.pdb
'/home/ondragahura/Work/Lab' has no suffix
> open2 "/home/ondragahura/Work/Lab
> Book/RNA_ligases_HMC/Modes/EcRnl2_Phyre_1s68a.pdb"
Chain information for EcRnl2_Phyre_1s68a.pdb #5
---
Chain | Description
| No description available
> open2 "/home/ondragahura/Work/Lab
> Book/RNA_ligases_HMC/Modes/EcRnl2_SwissModel_6vt4.pdb"
EcRnl2_SwissModel_6vt4.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for EcRnl2_SwissModel_6vt4.pdb #6
---
Chain | Description
A | No description available
> matchmaker #5,6 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 2hvq, chain A (#2) with EcRnl2_Phyre_1s68a.pdb, chain (blank) (#5),
sequence alignment score = 176.3
RMSD between 120 pruned atom pairs is 0.367 angstroms; (across all 197 pairs:
3.287)
Matchmaker 2hvq, chain A (#2) with EcRnl2_SwissModel_6vt4.pdb, chain A (#6),
sequence alignment score = 125.3
RMSD between 76 pruned atom pairs is 1.116 angstroms; (across all 181 pairs:
11.115)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #!2 models
> hide #4 models
> show #!2 models
> hide #5 models
> select #6/A:203
9 atoms, 8 bonds, 1 model selected
> select #6/A:205
7 atoms, 6 bonds, 1 model selected
> show sel atoms
> select clear
> select #6/A:93
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> select #6/A:49
8 atoms, 7 bonds, 1 model selected
> show sel atoms
> select #6/A:60
11 atoms, 10 bonds, 1 model selected
> show sel atoms
> select #6/A:21
6 atoms, 5 bonds, 1 model selected
> show sel atoms
> select #6/A:204
12 atoms, 12 bonds, 1 model selected
> show sel atoms
> hide sel atoms
> hide #!2 models
> hide #6 models
> show #!2 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> select #2/A:206
12 atoms, 12 bonds, 1 model selected
> hide sel atoms
> show #6 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> select #5:203
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> select clear
> select #5:93
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> select #5:7
12 atoms, 12 bonds, 1 model selected
> show sel atoms
> show #6 models
> hide #6 models
> show #6 models
> select #6/A:21@CB
1 atom, 1 model selected
> hide sel atoms
> select clear
> select #6/A:206
11 atoms, 10 bonds, 1 model selected
> show sel atoms
> select clear
> hide #6 models
> show #6 models
> save2 "/home/ondragahura/Work/Lab Book/RNA_ligases_HMC/RNA_lig.cxs"
> show #4 models
> select #4/A:77
11 atoms, 10 bonds, 1 model selected
> select up
42 atoms, 41 bonds, 1 model selected
> select up
3264 atoms, 2789 bonds, 1 model selected
> select up
16490 atoms, 16241 bonds, 6 models selected
Alignment identifier is 1
Alignment identifier is 1.D
Destroying pre-existing alignment with identifier 1.E
Alignment identifier is 1.E
Alignment identifier is 2
Alignment identifier is 3.D
Destroying pre-existing alignment with identifier 3.E
Alignment identifier is 3.E
Alignment identifier is 4.A
Missing or invalid "chains" argument: only initial part "#5" of atom specifier
valid
Alignment identifier is 3
Destroying pre-existing alignment with identifier 1.D
Alignment identifier is 1.D
Destroying pre-existing alignment with identifier 1.E
Alignment identifier is 1.E
Alignment identifier is 4
Destroying pre-existing alignment with identifier 3.D
Alignment identifier is 3.D
Destroying pre-existing alignment with identifier 3.E
Alignment identifier is 3.E
Destroying pre-existing alignment with identifier 4.A
Alignment identifier is 4.A
Missing or invalid "chains" argument: only initial part "#5" of atom specifier
valid
Drag select of 2 residues
> select clear
> hide #6 models
> hide #5 models
> hide #4 models
> show #4 models
> hide #!2 models
> show #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!2 models
> select #4/A:401@C4'
1 atom, 1 model selected
> select up
22 atoms, 24 bonds, 1 model selected
> contacts sel restrict #4 reveal true
77 contacts
> select ::name="HOH"
784 atoms, 4 models selected
> hide sek
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
> select #4/A:402@UNK
1 atom, 1 model selected
> hide sel
> show #!2 models
> select #4/A:312
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> select clear
> hide #!4 models
> show #!4 models
> show sel atoms
> hide sel atoms
> show #5 models
> hide #5 models
> show #5 models
> select up
2 atoms, 1 bond, 1 model selected
> hide sel atoms
> select #5:206@NH1
1 atom, 1 model selected
> select up
11 atoms, 10 bonds, 1 model selected
> hide sel atoms
> save2 "/home/ondragahura/Work/Lab Book/RNA_ligases_HMC/RNA_lig.cxs"
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #6 models
> select #6/A:20
7 atoms, 6 bonds, 1 model selected
> save2 "/home/ondragahura/Work/Lab Book/RNA_ligases_HMC/RNA_lig.cxs"
> hide #5 models
> hide #6 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #6 models
> show #5 models
> hide #5 models
> select #6/A:44
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> show #5 models
> hide #6 models
> select #5:44
9 atoms, 8 bonds, 1 model selected
> show sel atoms
> select clear
> select #5:113
11 atoms, 11 bonds, 1 model selected
> show sel atoms
> select #5:139
7 atoms, 6 bonds, 1 model selected
> show sel atoms
> select #5:205
7 atoms, 6 bonds, 1 model selected
> select #2/A:34
9 atoms, 8 bonds, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/E:236@C4'
1 atom, 1 model selected
> select up
22 atoms, 24 bonds, 1 model selected
> select down
1 atom, 1 model selected
> select up
22 atoms, 24 bonds, 1 model selected
> select up
268 atoms, 300 bonds, 1 model selected
> select down
22 atoms, 24 bonds, 1 model selected
> show #!2 models
> hide #!2 models
> hide #5 models
> save2 "/home/ondragahura/Work/Lab Book/RNA_ligases_HMC/RNA_lig.cxs"
> close session
> open 6zbb
Summary of feedback from opening 6zbb fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET #1 in chain 8
Atom H1 is not in the residue template for ASP #1 in chain K
Atom H1 is not in the residue template for ASP #1 in chain L
Atom H1 is not in the residue template for ASP #1 in chain M
Atom H1 is not in the residue template for ASP #1 in chain N
4 messages similar to the above omitted
Atom H2 is not in the residue template for PRO #1 in chain b
notes | Fetching compressed mmCIF 6zbb from
http://files.rcsb.org/download/6zbb.cif
Fetching CCD LHG from http://ligand-expo.rcsb.org/reports/L/LHG/LHG.cif
Fetching CCD M3L from http://ligand-expo.rcsb.org/reports/M/M3L/M3L.cif
6zbb title:
bovine ATP synthase Fo domain [more info...]
Chain information for 6zbb #1
---
Chain | Description
8 | ATP synthase protein 8
K L M N O P Q R | ATP synthase F(0) complex subunit C1, mitochondrial
a | ATP synthase subunit a
b | ATP synthase F(0) complex subunit B1, mitochondrial
d | ATP synthase subunit d, mitochondrial
e | ATP synthase subunit e, mitochondrial
f | ATP synthase subunit f, mitochondrial
g | ATP synthase subunit g, mitochondrial
j | ATP synthase subunit ATP5MPL, mitochondrial
k | ATP synthase membrane subunit DAPIT, mitochondrial
Non-standard residues in 6zbb #1
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
> show cartoons
> hide atoms
> select ::name="CDL"
546 atoms, 543 bonds, 1 model selected
> show sel atoms
> select ::name="LHG"
210 atoms, 208 bonds, 1 model selected
> show sel atoms
> open 6b2z
6b2z title:
Cryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase
[more info...]
Chain information for 6b2z #2
---
Chain | Description
0 1 2 3 4 5 6 7 8 9 B C D E F G H I J K | ATP synthase subunit c,
mitochondrial
A L | ATP synthase protein 8
M a | ATP synthase subunit a
N b | ATP synthase subunit b
O d | ATP synthase subunit d, mitochondrial
P e | ATP synthase subunit e, mitochondrial
Q f | ATP synthase subunit f, mitochondrial
R g | ATP synthase subunit g
S i | ATP synthase subunit j, mitochondrial
T k | ATP synthase subunit k, mitochondrial
> select #2
21436 atoms, 21822 bonds, 1 model selected
> hide sel atoms
> show sel cartoons
> matchmaker #1 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 6b2z, chain a (#2) with 6zbb, chain a (#1), sequence alignment
score = 487.1
RMSD between 142 pruned atom pairs is 1.012 angstroms; (across all 224 pairs:
6.311)
> select clear
> hide #1 models
Drag select of 1334 residues
> select up
10266 atoms, 10446 bonds, 1 model selected
> color sel grey
Drag select of
> show #1 models
> hide #1 models
> undo
> undo
> undo
> undo
Drag select of 1193 residues
> select up
9015 atoms, 9153 bonds, 1 model selected
> select up
10065 atoms, 10238 bonds, 1 model selected
> color sel grey
> color sel white
> select clear
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #2/k:26
4 atoms, 3 bonds, 1 model selected
> select up
56 atoms, 55 bonds, 1 model selected
> select up
180 atoms, 185 bonds, 1 model selected
> color sel white
> select clear
> select #1/f:35
7 atoms, 6 bonds, 1 model selected
> select up
279 atoms, 284 bonds, 1 model selected
> select up
1621 atoms, 1637 bonds, 1 model selected
> color sel yellow
> select clear
> select #1/d:116
22 atoms, 21 bonds, 1 model selected
> select up
86 atoms, 85 bonds, 1 model selected
> select up
893 atoms, 905 bonds, 1 model selected
> select #2/d:262
9 atoms, 8 bonds, 1 model selected
> select up
104 atoms, 104 bonds, 1 model selected
> select up
411 atoms, 418 bonds, 1 model selected
> open2
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/PL_all_190627.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.2.3610_ATPTB9.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.1690_su-f.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2180_ATPTB11.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2880_su-
> ij.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.720.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.3450_su-8.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.2930_su-d.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.3090_ATPTB12.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.6.590_ATPEG3.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.7.840_su-k.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.10.520_ATPTB1.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.600_ATPTB8.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.1270_ATPTB6.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.2245_su-b.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/subunit-a.pdb
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.1690_su-f.pdb
---
warnings | Ignored bad PDB record found on line 108
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 109
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 110
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 111
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 112
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2180_ATPTB11.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2880_su-ij.pdb
---
warnings | Ignored bad PDB record found on line 109
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 110
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 111
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 112
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 113
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.720.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.3450_su-8.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.2930_su-d.pdb
---
warnings | Ignored bad PDB record found on line 110
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 111
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 112
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 113
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 114
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.3090_ATPTB12.pdb
---
warnings | Ignored bad PDB record found on line 108
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 109
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 110
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 111
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 112
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.7.840_su-k.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 UNK V -23 UNK V -21
1 3
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.10.520_ATPTB1.pdb
---
warnings | Ignored bad PDB record found on line 124
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 125
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 126
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 127
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 128
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 VAL O 7 ASN O 14 1 8
Start residue of secondary structure not found: HELIX 2 2 PRO O 17 LYS O 42 1
26
Start residue of secondary structure not found: HELIX 3 3 THR O 46 VAL O 49 1
4
Start residue of secondary structure not found: HELIX 4 4 LEU O 76 THR O 78 1
3
Start residue of secondary structure not found: HELIX 5 5 GLN O 82 ALA O 107 1
26
10 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.600_ATPTB8.pdb
---
warnings | Ignored bad PDB record found on line 28
ALLOWED : 2.63 %
Ignored bad PDB record found on line 29
CIS-PROLINE : 0.574712643678
Ignored bad PDB record found on line 30
CIS-GENERAL : 0.0
Ignored bad PDB record found on line 31
FAVORED : 97.37 %
Ignored bad PDB record found on line 32
OUTLIERS : 0.00 %
16 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (30 )
Cannot find LINK/SSBOND residue CYS (24 )
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.1270_ATPTB6.pdb
---
warnings | Ignored bad PDB record found on line 110
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 111
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 112
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 113
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 114
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 6 6 TYR T 108 GLN T 128
1 21
Start residue of secondary structure not found: HELIX 7 7 VAL T 132 SER T 142
1 11
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/subunit-a.pdb
---
warnings | Ignored bad PDB record found on line 35
ALLOWED : 2.63 %
Ignored bad PDB record found on line 36
CIS-PROLINE : 0.574712643678
Ignored bad PDB record found on line 37
CIS-GENERAL : 0.0
Ignored bad PDB record found on line 38
FAVORED : 97.37 %
Ignored bad PDB record found on line 39
OUTLIERS : 0.00 %
16 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 TRP G 36 TYR G 46 1
11
Start residue of secondary structure not found: HELIX 2 2 ASN G 59 MET G 62 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU G 75 LEU G 97 1
23
End residue of secondary structure not found: HELIX 4 4 LEU G 108 LEU G 129 1
22
Start residue of secondary structure not found: HELIX 5 5 PHE G 133 LEU G 138
1 6
Start residue of secondary structure not found: HELIX 6 6 VAL G 147 PHE G 197
1 51
Start residue of secondary structure not found: HELIX 7 7 TYR G 200 VAL G 202
1 3
Start residue of secondary structure not found: HELIX 8 8 PHE G 207 PHE G 250
1 44
Cannot find LINK/SSBOND residue CYS (30 )
Cannot find LINK/SSBOND residue CYS (24 )
Chain information for Tb927.2.3610_ATPTB9.pdb #4
---
Chain | Description
H | No description available
Tb927.3.1690_su-f.pdb title:
\--- [more info...]
Chain information for Tb927.3.1690_su-f.pdb #5
---
Chain | Description
S | No description available
Tb927.3.2180_ATPTB11.pdb title:
\--- [more info...]
Chain information for Tb927.3.2180_ATPTB11.pdb #6
---
Chain | Description
d | No description available
Tb927.3.2880_su-ij.pdb title:
\--- [more info...]
Chain information for Tb927.3.2880_su-ij.pdb #7
---
Chain | Description
a | No description available
Tb927.4.720.pdb title:
\--- [more info...]
Chain information for Tb927.4.720.pdb #8
---
Chain | Description
k | No description available
Tb927.4.3450_su-8.pdb title:
\--- [more info...]
Chain information for Tb927.4.3450_su-8.pdb #9
---
Chain | Description
f | No description available
Tb927.5.2930_su-d.pdb title:
\--- [more info...]
Chain information for Tb927.5.2930_su-d.pdb #10
---
Chain | Description
C | No description available
L | No description available
Tb927.5.3090_ATPTB12.pdb title:
\--- [more info...]
Chain information for Tb927.5.3090_ATPTB12.pdb #11
---
Chain | Description
r | No description available
Chain information for Tb927.6.590_ATPEG3.pdb #12
---
Chain | Description
| No description available
Tb927.7.840_su-k.pdb title:
\--- [more info...]
Chain information for Tb927.7.840_su-k.pdb #13
---
Chain | Description
V | No description available
Tb927.10.520_ATPTB1.pdb title:
\--- [more info...]
Chain information for Tb927.10.520_ATPTB1.pdb #14
---
Chain | Description
O | No description available
Chain information for Tb927.11.600_ATPTB8.pdb #15
---
Chain | Description
I | No description available
Tb927.11.1270_ATPTB6.pdb title:
\--- [more info...]
Chain information for Tb927.11.1270_ATPTB6.pdb #16
---
Chain | Description
T | No description available
Chain information for Tb927.11.2245_su-b.pdb #17
---
Chain | Description
| No description available
Chain information for subunit-a.pdb #18
---
Chain | Description
G | No description available
> hide #2 models
> hide #1 models
> close #3
> rename #4-18 id #4
> show #2 models
> hide #!4 models
> matchmaker #4.15 to #2/a bring #4.1-14
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 6b2z, chain a (#2) with subunit-a.pdb, chain G (#4.15), sequence
alignment score = 282.1
RMSD between 84 pruned atom pairs is 1.132 angstroms; (across all 216 pairs:
8.649)
> show #!4 models
> hide #2 models
> show #1 models
> dssp
> select #1/b:108
19 atoms, 18 bonds, 1 model selected
> select up
560 atoms, 560 bonds, 1 model selected
> select up
2152 atoms, 2171 bonds, 1 model selected
> select up
21505 atoms, 21712 bonds, 1 model selected
> select down
2152 atoms, 2171 bonds, 1 model selected
> select clear
> select #4.2/S:60
12 atoms, 12 bonds, 1 model selected
> select up
210 atoms, 221 bonds, 1 model selected
> select up
1145 atoms, 1183 bonds, 1 model selected
> select up
17741 atoms, 18275 bonds, 15 models selected
> select down
1145 atoms, 1183 bonds, 1 model selected
> select clear
> select #1/b:60
10 atoms, 9 bonds, 1 model selected
> select up
294 atoms, 297 bonds, 1 model selected
> select up
2152 atoms, 2171 bonds, 1 model selected
> select down
294 atoms, 297 bonds, 1 model selected
> select up
2152 atoms, 2171 bonds, 1 model selected
> open2 /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/CDL2.pdb
> hide #3 models
> show #3 models
> close #3
> show #2 models
> open2
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/tryp_membrane_all.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/tryp_membrane_all_2.pdb
Chain information for tryp_membrane_all.pdb #3
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
I | No description available
L | No description available
O | No description available
S | No description available
T | No description available
V | No description available
a | No description available
d | No description available
f | No description available
k | No description available
r | No description available
Chain information for tryp_membrane_all_2.pdb #5
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
I | No description available
L | No description available
O | No description available
S | No description available
T | No description available
V | No description available
a | No description available
d | No description available
f | No description available
k | No description available
r | No description available
> select #3
16533 atoms, 17053 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> select #5
16533 atoms, 17053 bonds, 1 model selected
> show sel cartoons
> hide sel atoms
> hide #!4 models
> hide #2 models
> matchmaker #5/g to #1/a
No molecules/chains to match specified
> hide #1 models
> hide #3 models
> hide #5 models
> show #1 models
> show #3 models
> show #5 models
> matchmaker #5/G to #1/a bring #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 6zbb, chain a (#1) with tryp_membrane_all_2.pdb, chain G (#5),
sequence alignment score = 208.1
RMSD between 120 pruned atom pairs is 1.202 angstroms; (across all 191 pairs:
7.851)
> select clear
> select ::name="CDL"
546 atoms, 543 bonds, 1 model selected
> show sel atoms
> hide #1 models
> show #1 models
> matchmaker #5/k to #1/b bring #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 6zbb, chain b (#1) with tryp_membrane_all_2.pdb, chain k (#5),
sequence alignment score = 25.4
RMSD between 8 pruned atom pairs is 0.881 angstroms; (across all 30 pairs:
21.856)
> matchmaker #5/G to #1/a bring #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 6zbb, chain a (#1) with tryp_membrane_all_2.pdb, chain G (#5),
sequence alignment score = 208.1
RMSD between 120 pruned atom pairs is 1.202 angstroms; (across all 191 pairs:
7.851)
> select #5/A:18
7 atoms, 7 bonds, 1 model selected
> select up
208 atoms, 219 bonds, 1 model selected
> select up
531 atoms, 555 bonds, 1 model selected
> select #5/k:83
8 atoms, 7 bonds, 1 model selected
> select up
187 atoms, 195 bonds, 1 model selected
> select up
683 atoms, 706 bonds, 1 model selected
Alignment identifier is 5.k
> select clear
> ribbon #4.5
> hide #4.5 models
> show #4.5 models
> hide #4.5 models
> show #4.5 models
> hide #4.5 models
> show #4.5 models
> hide #4.5 models
> select #5/k:97
12 atoms, 12 bonds, 1 model selected
> select up
187 atoms, 195 bonds, 1 model selected
> select up
683 atoms, 706 bonds, 1 model selected
> hide #1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #1 models
> hide #1 models
> show #1 models
> select #1/b:37
19 atoms, 18 bonds, 1 model selected
> select up
232 atoms, 234 bonds, 1 model selected
> select up
2152 atoms, 2171 bonds, 1 model selected
> hide #1 models
> select #5/H:111
11 atoms, 11 bonds, 1 model selected
> select up
214 atoms, 217 bonds, 1 model selected
Alignment identifier is 5.H
> show #1 models
> select clear
> select #1/g:83
24 atoms, 25 bonds, 1 model selected
> select up
57 atoms, 58 bonds, 1 model selected
> select up
1291 atoms, 1308 bonds, 1 model selected
Alignment identifier is 1.g
> hide #1 models
> show #1 models
> hide #1 models
> select #5/I:24
10 atoms, 9 bonds, 1 model selected
> select up
524 atoms, 531 bonds, 1 model selected
Alignment identifier is 5.I
> show #1 models
> select #1/e:21
7 atoms, 6 bonds, 1 model selected
> select up
848 atoms, 854 bonds, 1 model selected
Alignment identifier is 1.e
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> close session
> open2
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.2.3610_ATPTB9.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.1690_su-f.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2180_ATPTB11.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2880_su-
> ij.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.720.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.3450_su-8.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.2930_su-d.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.3090_ATPTB12.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.6.590_ATPEG3.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.7.840_su-k.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.10.520_ATPTB1.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.600_ATPTB8.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.1270_ATPTB6.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.2245_su-b.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/subunit-a.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/tryp_membrane_all.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/tryp_membrane_all_2.pdb
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.1690_su-f.pdb
---
warnings | Ignored bad PDB record found on line 108
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 109
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 110
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 111
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 112
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2180_ATPTB11.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2880_su-ij.pdb
---
warnings | Ignored bad PDB record found on line 109
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 110
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 111
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 112
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 113
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.720.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.3450_su-8.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.2930_su-d.pdb
---
warnings | Ignored bad PDB record found on line 110
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 111
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 112
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 113
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 114
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.3090_ATPTB12.pdb
---
warnings | Ignored bad PDB record found on line 108
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 109
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 110
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 111
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 112
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.7.840_su-k.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 UNK V -23 UNK V -21
1 3
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.10.520_ATPTB1.pdb
---
warnings | Ignored bad PDB record found on line 124
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 125
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 126
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 127
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 128
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 VAL O 7 ASN O 14 1 8
Start residue of secondary structure not found: HELIX 2 2 PRO O 17 LYS O 42 1
26
Start residue of secondary structure not found: HELIX 3 3 THR O 46 VAL O 49 1
4
Start residue of secondary structure not found: HELIX 4 4 LEU O 76 THR O 78 1
3
Start residue of secondary structure not found: HELIX 5 5 GLN O 82 ALA O 107 1
26
10 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.600_ATPTB8.pdb
---
warnings | Ignored bad PDB record found on line 28
ALLOWED : 2.63 %
Ignored bad PDB record found on line 29
CIS-PROLINE : 0.574712643678
Ignored bad PDB record found on line 30
CIS-GENERAL : 0.0
Ignored bad PDB record found on line 31
FAVORED : 97.37 %
Ignored bad PDB record found on line 32
OUTLIERS : 0.00 %
16 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (30 )
Cannot find LINK/SSBOND residue CYS (24 )
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.1270_ATPTB6.pdb
---
warnings | Ignored bad PDB record found on line 110
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 111
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 112
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 113
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 114
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 6 6 TYR T 108 GLN T 128
1 21
Start residue of secondary structure not found: HELIX 7 7 VAL T 132 SER T 142
1 11
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/subunit-a.pdb
---
warnings | Ignored bad PDB record found on line 35
ALLOWED : 2.63 %
Ignored bad PDB record found on line 36
CIS-PROLINE : 0.574712643678
Ignored bad PDB record found on line 37
CIS-GENERAL : 0.0
Ignored bad PDB record found on line 38
FAVORED : 97.37 %
Ignored bad PDB record found on line 39
OUTLIERS : 0.00 %
16 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 TRP G 36 TYR G 46 1
11
Start residue of secondary structure not found: HELIX 2 2 ASN G 59 MET G 62 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU G 75 LEU G 97 1
23
End residue of secondary structure not found: HELIX 4 4 LEU G 108 LEU G 129 1
22
Start residue of secondary structure not found: HELIX 5 5 PHE G 133 LEU G 138
1 6
Start residue of secondary structure not found: HELIX 6 6 VAL G 147 PHE G 197
1 51
Start residue of secondary structure not found: HELIX 7 7 TYR G 200 VAL G 202
1 3
Start residue of secondary structure not found: HELIX 8 8 PHE G 207 PHE G 250
1 44
Cannot find LINK/SSBOND residue CYS (30 )
Cannot find LINK/SSBOND residue CYS (24 )
Chain information for Tb927.2.3610_ATPTB9.pdb #1
---
Chain | Description
H | No description available
Tb927.3.1690_su-f.pdb title:
\--- [more info...]
Chain information for Tb927.3.1690_su-f.pdb #2
---
Chain | Description
S | No description available
Tb927.3.2180_ATPTB11.pdb title:
\--- [more info...]
Chain information for Tb927.3.2180_ATPTB11.pdb #3
---
Chain | Description
d | No description available
Tb927.3.2880_su-ij.pdb title:
\--- [more info...]
Chain information for Tb927.3.2880_su-ij.pdb #4
---
Chain | Description
a | No description available
Tb927.4.720.pdb title:
\--- [more info...]
Chain information for Tb927.4.720.pdb #5
---
Chain | Description
k | No description available
Tb927.4.3450_su-8.pdb title:
\--- [more info...]
Chain information for Tb927.4.3450_su-8.pdb #6
---
Chain | Description
f | No description available
Tb927.5.2930_su-d.pdb title:
\--- [more info...]
Chain information for Tb927.5.2930_su-d.pdb #7
---
Chain | Description
C | No description available
L | No description available
Tb927.5.3090_ATPTB12.pdb title:
\--- [more info...]
Chain information for Tb927.5.3090_ATPTB12.pdb #8
---
Chain | Description
r | No description available
Chain information for Tb927.6.590_ATPEG3.pdb #9
---
Chain | Description
| No description available
Tb927.7.840_su-k.pdb title:
\--- [more info...]
Chain information for Tb927.7.840_su-k.pdb #10
---
Chain | Description
V | No description available
Tb927.10.520_ATPTB1.pdb title:
\--- [more info...]
Chain information for Tb927.10.520_ATPTB1.pdb #11
---
Chain | Description
O | No description available
Chain information for Tb927.11.600_ATPTB8.pdb #12
---
Chain | Description
I | No description available
Tb927.11.1270_ATPTB6.pdb title:
\--- [more info...]
Chain information for Tb927.11.1270_ATPTB6.pdb #13
---
Chain | Description
T | No description available
Chain information for Tb927.11.2245_su-b.pdb #14
---
Chain | Description
| No description available
Chain information for subunit-a.pdb #15
---
Chain | Description
G | No description available
Chain information for tryp_membrane_all.pdb #16
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
I | No description available
L | No description available
O | No description available
S | No description available
T | No description available
V | No description available
a | No description available
d | No description available
f | No description available
k | No description available
r | No description available
Chain information for tryp_membrane_all_2.pdb #17
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
I | No description available
L | No description available
O | No description available
S | No description available
T | No description available
V | No description available
a | No description available
d | No description available
f | No description available
k | No description available
r | No description available
> close session
> open2
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.2.3610_ATPTB9.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.1690_su-f.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2180_ATPTB11.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2880_su-
> ij.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.720.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.3450_su-8.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.2930_su-d.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.3090_ATPTB12.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.6.590_ATPEG3.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.7.840_su-k.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.10.520_ATPTB1.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.600_ATPTB8.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.1270_ATPTB6.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.2245_su-b.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/subunit-a.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/tryp_membrane_all.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/tryp_membrane_all_2.pdb
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.1690_su-f.pdb
---
warnings | Ignored bad PDB record found on line 108
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 109
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 110
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 111
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 112
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2180_ATPTB11.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.3.2880_su-ij.pdb
---
warnings | Ignored bad PDB record found on line 109
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 110
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 111
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 112
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 113
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.720.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.4.3450_su-8.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.2930_su-d.pdb
---
warnings | Ignored bad PDB record found on line 110
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 111
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 112
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 113
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 114
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.5.3090_ATPTB12.pdb
---
warnings | Ignored bad PDB record found on line 108
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 109
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 110
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 111
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 112
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.7.840_su-k.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 108
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 109
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 110
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 111
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 UNK V -23 UNK V -21
1 3
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.10.520_ATPTB1.pdb
---
warnings | Ignored bad PDB record found on line 124
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 125
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 126
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 127
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 128
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 VAL O 7 ASN O 14 1 8
Start residue of secondary structure not found: HELIX 2 2 PRO O 17 LYS O 42 1
26
Start residue of secondary structure not found: HELIX 3 3 THR O 46 VAL O 49 1
4
Start residue of secondary structure not found: HELIX 4 4 LEU O 76 THR O 78 1
3
Start residue of secondary structure not found: HELIX 5 5 GLN O 82 ALA O 107 1
26
10 messages similar to the above omitted
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.600_ATPTB8.pdb
---
warnings | Ignored bad PDB record found on line 28
ALLOWED : 2.63 %
Ignored bad PDB record found on line 29
CIS-PROLINE : 0.574712643678
Ignored bad PDB record found on line 30
CIS-GENERAL : 0.0
Ignored bad PDB record found on line 31
FAVORED : 97.37 %
Ignored bad PDB record found on line 32
OUTLIERS : 0.00 %
16 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (30 )
Cannot find LINK/SSBOND residue CYS (24 )
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/Tb927.11.1270_ATPTB6.pdb
---
warnings | Ignored bad PDB record found on line 110
LINKR VAL E 8 LEU E 10 gap
Ignored bad PDB record found on line 111
LINKR ASN E 46 LYS E 49 gap
Ignored bad PDB record found on line 112
LINKR ALA E 55 LEU E 61 gap
Ignored bad PDB record found on line 113
LINKR LYS F 49 ASN F 53 gap
Ignored bad PDB record found on line 114
LINKR ARG M 218 ASP M 223 gap
6 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 6 6 TYR T 108 GLN T 128
1 21
Start residue of secondary structure not found: HELIX 7 7 VAL T 132 SER T 142
1 11
Summary of feedback from opening
/home/ondragahura/DATA/ATP_synthase/Models/Fo_membrane/subunit-a.pdb
---
warnings | Ignored bad PDB record found on line 35
ALLOWED : 2.63 %
Ignored bad PDB record found on line 36
CIS-PROLINE : 0.574712643678
Ignored bad PDB record found on line 37
CIS-GENERAL : 0.0
Ignored bad PDB record found on line 38
FAVORED : 97.37 %
Ignored bad PDB record found on line 39
OUTLIERS : 0.00 %
16 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 TRP G 36 TYR G 46 1
11
Start residue of secondary structure not found: HELIX 2 2 ASN G 59 MET G 62 1
4
Start residue of secondary structure not found: HELIX 3 3 LEU G 75 LEU G 97 1
23
End residue of secondary structure not found: HELIX 4 4 LEU G 108 LEU G 129 1
22
Start residue of secondary structure not found: HELIX 5 5 PHE G 133 LEU G 138
1 6
Start residue of secondary structure not found: HELIX 6 6 VAL G 147 PHE G 197
1 51
Start residue of secondary structure not found: HELIX 7 7 TYR G 200 VAL G 202
1 3
Start residue of secondary structure not found: HELIX 8 8 PHE G 207 PHE G 250
1 44
Cannot find LINK/SSBOND residue CYS (30 )
Cannot find LINK/SSBOND residue CYS (24 )
Chain information for Tb927.2.3610_ATPTB9.pdb #1
---
Chain | Description
H | No description available
Tb927.3.1690_su-f.pdb title:
\--- [more info...]
Chain information for Tb927.3.1690_su-f.pdb #2
---
Chain | Description
S | No description available
Tb927.3.2180_ATPTB11.pdb title:
\--- [more info...]
Chain information for Tb927.3.2180_ATPTB11.pdb #3
---
Chain | Description
d | No description available
Tb927.3.2880_su-ij.pdb title:
\--- [more info...]
Chain information for Tb927.3.2880_su-ij.pdb #4
---
Chain | Description
a | No description available
Tb927.4.720.pdb title:
\--- [more info...]
Chain information for Tb927.4.720.pdb #5
---
Chain | Description
k | No description available
Tb927.4.3450_su-8.pdb title:
\--- [more info...]
Chain information for Tb927.4.3450_su-8.pdb #6
---
Chain | Description
f | No description available
Tb927.5.2930_su-d.pdb title:
\--- [more info...]
Chain information for Tb927.5.2930_su-d.pdb #7
---
Chain | Description
C | No description available
L | No description available
Tb927.5.3090_ATPTB12.pdb title:
\--- [more info...]
Chain information for Tb927.5.3090_ATPTB12.pdb #8
---
Chain | Description
r | No description available
Chain information for Tb927.6.590_ATPEG3.pdb #9
---
Chain | Description
| No description available
Tb927.7.840_su-k.pdb title:
\--- [more info...]
Chain information for Tb927.7.840_su-k.pdb #10
---
Chain | Description
V | No description available
Tb927.10.520_ATPTB1.pdb title:
\--- [more info...]
Chain information for Tb927.10.520_ATPTB1.pdb #11
---
Chain | Description
O | No description available
Chain information for Tb927.11.600_ATPTB8.pdb #12
---
Chain | Description
I | No description available
Tb927.11.1270_ATPTB6.pdb title:
\--- [more info...]
Chain information for Tb927.11.1270_ATPTB6.pdb #13
---
Chain | Description
T | No description available
Chain information for Tb927.11.2245_su-b.pdb #14
---
Chain | Description
| No description available
Chain information for subunit-a.pdb #15
---
Chain | Description
G | No description available
Chain information for tryp_membrane_all.pdb #16
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
I | No description available
L | No description available
O | No description available
S | No description available
T | No description available
V | No description available
a | No description available
d | No description available
f | No description available
k | No description available
r | No description available
Chain information for tryp_membrane_all_2.pdb #17
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
I | No description available
L | No description available
O | No description available
S | No description available
T | No description available
V | No description available
a | No description available
d | No description available
f | No description available
k | No description available
r | No description available
> hide #!7 models
> show #!7 models
> show cartoons
> hide atoms
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #16 models
> show #16 models
> hide #17 models
> show #17 models
> hide #!7 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide #16 models
> hide #17 models
> show #!7 models
> dssp
> rename #1-17 id #1
> rename #1 Tb_membrane
> open 6tvd
Fetching url http://files.rcsb.org/download/6tvd.cif failed: HTTP Error 404:
Not Found
> fetch 6tvd
Unknown command: fetch 6tvd
> open 6tdv
Summary of feedback from opening 6tdv fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET #1 in chain F
Atom H1 is not in the residue template for LEU #1 in chain L
Atom H1 is not in the residue template for MET #1 in chain T
Atom H1 is not in the residue template for MET #1 in chain f
Atom H1 is not in the residue template for LEU #1 in chain l
1 messages similar to the above omitted
6tdv title:
Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, membrane
region [more info...]
Chain information for 6tdv #2
---
Chain | Description
A a | ATPTB1
B b | ATPTB3
D d | ATPTB6
E e | ATPTB12
F f | subunit a
G g | subunit b
H h | subunit d
I i | subunit f
J j | subunit i/j
K k | subunit k
L l | subunit 8
M m | ATPEG1
N n | ATPEG2
O o | ATPEG3
P p | ATPEG4
Q q | ATPEG5
R r | ATPEG6
S s | ATPEG7
T t | ATPEG8
Non-standard residues in 6tdv #2
---
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
LMT — dodecyl-β-D-maltoside
LPP — 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate
(1,2-dipalmitoyl-Sn-glycero-3-phosphate; L-B,G-dipalmitoyl-A-phosphatidic acid
disodium salt; 3-Sn-phosphatidic acid; 1,2-dipalmitoyldisodium salt)
TRT — fragment of triton X-100
(1-{2-[2-(2-methoxyethoxy)ethoxy]ethoxy}-4-(1,1,3,3-tetramethylbutyl)benzene)
> matchmaker #2 to #1
Specify a single 'to' model only
> matchmaker #2 to #1.16
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 tryp_membrane_all.pdb, chain O (#1.16) with 6tdv, chain A (#2),
sequence alignment score = 316.7
RMSD between 112 pruned atom pairs is 1.265 angstroms; (across all 354 pairs:
24.539)
> show #1.1-6,8-15#!2#!1.7 cartoons
> hide #1.1-6,8-15#!2#!1.7 atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> matchmaker #2/f to #1.15/G
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 subunit-a.pdb, chain G (#1.15) with 6tdv, chain f (#2), sequence
alignment score = 219.1
RMSD between 19 pruned atom pairs is 1.516 angstroms; (across all 205 pairs:
12.110)
> show #!2 models
> hide #!1 models
> select #2/f:178
24 atoms, 23 bonds, 1 model selected
> select up
602 atoms, 612 bonds, 1 model selected
> select up
4764 atoms, 4830 bonds, 1 model selected
> color sel green
> select #2/F:62
19 atoms, 18 bonds, 1 model selected
> select up
389 atoms, 392 bonds, 1 model selected
> select up
4761 atoms, 4826 bonds, 1 model selected
> color sel green
> select clear
> select #2/h:207
11 atoms, 10 bonds, 1 model selected
> select up
88 atoms, 90 bonds, 1 model selected
> select up
6165 atoms, 6244 bonds, 1 model selected
> select up
6253 atoms, 6334 bonds, 1 model selected
> select up
12330 atoms, 12488 bonds, 1 model selected
> color sel firebrick
> select clear
> show #!1 models
> lighting simple
> hide #!1 models
> open 6tdu
Summary of feedback from opening 6tdu fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET #1 in chain F
Atom H1 is not in the residue template for LEU #1 in chain L
Atom H1 is not in the residue template for MET #1 in chain T
Atom H1 is not in the residue template for MET #1 in chain f
Atom H1 is not in the residue template for LEU #1 in chain l
1 messages similar to the above omitted
6tdu title:
Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, full dimer,
rotational states 1 [more info...]
Chain information for 6tdu #3
---
Chain | Description
A a | ATPTB1
AA AB AC BA BB BC | ATP synthase subunit α
AD AE AF BD BE BF | ATP synthase subunit β
AG BG | ATP synthase subunit γ
AH BH | ATP synthase subunit δ
AI BI | ATP synthase subunit ε
AJ AK AL BJ BK BL | p18
AM BM | oligomycin sensitivity conferring protein (OSCP)
AN BN | inhibitor of F1 (IF1)
AO AP AQ AR AS AT AU AV AW AX BO BP BQ BR BS BT BU BV BW BX | ATP synthase
subunit c
B b | ATPTB3
C c | ATPTB4
D d | ATPTB6
E e | ATPTB12
F f | ATP synthase subunit a
G g | ATP synthase subunit b
H h | ATP synthase subunit d
I i | ATP synthase subunit f
J j | ATP synthase subunit i/j
K k | ATP synthase subunit k
L l | ATP synthase subunit 8
M m | ATPEG1
N n | ATPEG2
O o | ATPEG3
P p | ATPEG4
Q q | ATPEG5
R r | ATPEG6
S s | ATPEG7
T t | ATPEG8
Non-standard residues in 6tdu #3
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
LMT — dodecyl-β-D-maltoside
LPP — 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate
(1,2-dipalmitoyl-Sn-glycero-3-phosphate; L-B,G-dipalmitoyl-A-phosphatidic acid
disodium salt; 3-Sn-phosphatidic acid; 1,2-dipalmitoyldisodium salt)
MG — magnesium ion
TRT — fragment of triton X-100
(1-{2-[2-(2-methoxyethoxy)ethoxy]ethoxy}-4-(1,1,3,3-tetramethylbutyl)benzene)
> matchmaker #3 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 6tdv, chain A (#2) with 6tdu, chain A (#3), sequence alignment
score = 2517.1
RMSD between 486 pruned atom pairs is 0.269 angstroms; (across all 486 pairs:
0.269)
> show #!2-3 cartoons
> hide #!2-3 atoms
> hide #2.1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
Drag select of 4228 residues, 3 pseudobonds
> select up
69455 atoms, 70014 bonds, 3 pseudobonds, 3 models selected
> select up
86970 atoms, 87748 bonds, 3 pseudobonds, 3 models selected
Drag select of 5204 residues, 4 pseudobonds
> select up
171358 atoms, 172847 bonds, 7 pseudobonds, 3 models selected
> select up
199439 atoms, 201289 bonds, 7 pseudobonds, 3 models selected
> select down
171358 atoms, 172847 bonds, 7 pseudobonds, 3 models selected
> select clear
> select
> #3/A,a,AA,AB,AC,BA,BB,BC,AD,AE,AF,BD,BE,BF,AG,BG,AH,BH,AI,BI,AJ,AK,AL,BJ,BK,BL,AM,BM,B,b,C,c,D,d,E,e,F,f
186168 atoms, 187865 bonds, 43 pseudobonds, 3 models selected
> color sel royalblue
> select clear
> select #3/G:96
10 atoms, 9 bonds, 1 model selected
> select up
443 atoms, 444 bonds, 1 model selected
> select up
1925 atoms, 1947 bonds, 1 model selected
> select #2/B:127
19 atoms, 18 bonds, 1 model selected
> select up
440 atoms, 441 bonds, 1 model selected
> select up
494 atoms, 495 bonds, 1 model selected
> select up
95420 atoms, 96673 bonds, 1 model selected
> select clear
> select #3/H:285
16 atoms, 15 bonds, 1 model selected
> select up
191 atoms, 192 bonds, 1 model selected
> select up
7302 atoms, 7392 bonds, 1 model selected
> select up
7351 atoms, 7440 bonds, 1 model selected
> select up
14604 atoms, 14784 bonds, 1 model selected
> color sel royalblue
> select clear
> hide #!2 models
> select #3/BN:67
15 atoms, 14 bonds, 1 model selected
> ~ribbon #3/AN,BN
> save2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> toolshed show "Side View"
Drag select of 284 residues
> select up
6184 atoms, 6206 bonds, 1 model selected
> select up
16792 atoms, 16956 bonds, 1 model selected
> select down
16773 atoms, 16956 bonds, 1 model selected
> select down
16773 atoms, 16956 bonds, 1 model selected
> select down
16773 atoms, 16956 bonds, 1 model selected
> select up
16792 atoms, 16956 bonds, 1 model selected
> select down
16773 atoms, 16956 bonds, 1 model selected
> select down
16773 atoms, 16956 bonds, 1 model selected
> select clear
Drag select of 232 residues
> select up
6154 atoms, 6197 bonds, 1 model selected
> select up
11911 atoms, 12011 bonds, 1 model selected
> color sel royalblue
> select clear
Drag select of 99 residues
> select up
4290 atoms, 4320 bonds, 1 model selected
> select up
11911 atoms, 12011 bonds, 1 model selected
> select up
271331 atoms, 274070 bonds, 1 model selected
> select down
11911 atoms, 12011 bonds, 1 model selected
> color sel royalblue
> select clear
> select bycol
Expected an objects specifier or a keyword
> select #1/D,d
3381 atoms, 3495 bonds, 3 models selected
> select #3/D,d
6698 atoms, 6774 bonds, 1 model selected
> select #3/A:131
15 atoms, 14 bonds, 1 model selected
> select up
286 atoms, 289 bonds, 1 model selected
> select up
8684 atoms, 8779 bonds, 1 model selected
> select up
9198 atoms, 9303 bonds, 1 model selected
> select up
12033 atoms, 12166 bonds, 1 model selected
> save2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> split #3
Chain information for 6tdu A #3.1
---
Chain | Description
A | No description available
Chain information for 6tdu AA #3.2
---
Chain | Description
AA | No description available
Chain information for 6tdu AB #3.3
---
Chain | Description
AB | No description available
Chain information for 6tdu AC #3.4
---
Chain | Description
AC | No description available
Chain information for 6tdu AD #3.5
---
Chain | Description
AD | No description available
Chain information for 6tdu AE #3.6
---
Chain | Description
AE | No description available
Chain information for 6tdu AF #3.7
---
Chain | Description
AF | No description available
Chain information for 6tdu AG #3.8
---
Chain | Description
AG | No description available
Chain information for 6tdu AH #3.9
---
Chain | Description
AH | No description available
Chain information for 6tdu AI #3.10
---
Chain | Description
AI | No description available
Chain information for 6tdu AJ #3.11
---
Chain | Description
AJ | No description available
Chain information for 6tdu AK #3.12
---
Chain | Description
AK | No description available
Chain information for 6tdu AL #3.13
---
Chain | Description
AL | No description available
Chain information for 6tdu AM #3.14
---
Chain | Description
AM | No description available
Chain information for 6tdu AN #3.15
---
Chain | Description
AN | No description available
Chain information for 6tdu AO #3.16
---
Chain | Description
AO | No description available
Chain information for 6tdu AP #3.17
---
Chain | Description
AP | No description available
Chain information for 6tdu AQ #3.18
---
Chain | Description
AQ | No description available
Chain information for 6tdu AR #3.19
---
Chain | Description
AR | No description available
Chain information for 6tdu AS #3.20
---
Chain | Description
AS | No description available
Chain information for 6tdu AT #3.21
---
Chain | Description
AT | No description available
Chain information for 6tdu AU #3.22
---
Chain | Description
AU | No description available
Chain information for 6tdu AV #3.23
---
Chain | Description
AV | No description available
Chain information for 6tdu AW #3.24
---
Chain | Description
AW | No description available
Chain information for 6tdu AX #3.25
---
Chain | Description
AX | No description available
Chain information for 6tdu B #3.26
---
Chain | Description
B | No description available
Chain information for 6tdu BA #3.27
---
Chain | Description
BA | No description available
Chain information for 6tdu BB #3.28
---
Chain | Description
BB | No description available
Chain information for 6tdu BC #3.29
---
Chain | Description
BC | No description available
Chain information for 6tdu BD #3.30
---
Chain | Description
BD | No description available
Chain information for 6tdu BE #3.31
---
Chain | Description
BE | No description available
Chain information for 6tdu BF #3.32
---
Chain | Description
BF | No description available
Chain information for 6tdu BG #3.33
---
Chain | Description
BG | No description available
Chain information for 6tdu BH #3.34
---
Chain | Description
BH | No description available
Chain information for 6tdu BI #3.35
---
Chain | Description
BI | No description available
Chain information for 6tdu BJ #3.36
---
Chain | Description
BJ | No description available
Chain information for 6tdu BK #3.37
---
Chain | Description
BK | No description available
Chain information for 6tdu BL #3.38
---
Chain | Description
BL | No description available
Chain information for 6tdu BM #3.39
---
Chain | Description
BM | No description available
Chain information for 6tdu BN #3.40
---
Chain | Description
BN | No description available
Chain information for 6tdu BO #3.41
---
Chain | Description
BO | No description available
Chain information for 6tdu BP #3.42
---
Chain | Description
BP | No description available
Chain information for 6tdu BQ #3.43
---
Chain | Description
BQ | No description available
Chain information for 6tdu BR #3.44
---
Chain | Description
BR | No description available
Chain information for 6tdu BS #3.45
---
Chain | Description
BS | No description available
Chain information for 6tdu BT #3.46
---
Chain | Description
BT | No description available
Chain information for 6tdu BU #3.47
---
Chain | Description
BU | No description available
Chain information for 6tdu BV #3.48
---
Chain | Description
BV | No description available
Chain information for 6tdu BW #3.49
---
Chain | Description
BW | No description available
Chain information for 6tdu BX #3.50
---
Chain | Description
BX | No description available
Chain information for 6tdu C #3.51
---
Chain | Description
C | No description available
Chain information for 6tdu D #3.52
---
Chain | Description
D | No description available
Chain information for 6tdu E #3.53
---
Chain | Description
E | No description available
Chain information for 6tdu F #3.54
---
Chain | Description
F | No description available
Chain information for 6tdu G #3.55
---
Chain | Description
G | No description available
Chain information for 6tdu H #3.56
---
Chain | Description
H | No description available
Chain information for 6tdu I #3.57
---
Chain | Description
I | No description available
Chain information for 6tdu J #3.58
---
Chain | Description
J | No description available
Chain information for 6tdu K #3.59
---
Chain | Description
K | No description available
Chain information for 6tdu L #3.60
---
Chain | Description
L | No description available
Chain information for 6tdu M #3.61
---
Chain | Description
M | No description available
Chain information for 6tdu N #3.62
---
Chain | Description
N | No description available
Chain information for 6tdu O #3.63
---
Chain | Description
O | No description available
Chain information for 6tdu P #3.64
---
Chain | Description
P | No description available
Chain information for 6tdu Q #3.65
---
Chain | Description
Q | No description available
Chain information for 6tdu R #3.66
---
Chain | Description
R | No description available
Chain information for 6tdu S #3.67
---
Chain | Description
S | No description available
Chain information for 6tdu T #3.68
---
Chain | Description
T | No description available
Chain information for 6tdu a #3.69
---
Chain | Description
a | No description available
Chain information for 6tdu b #3.70
---
Chain | Description
b | No description available
Chain information for 6tdu c #3.71
---
Chain | Description
c | No description available
Chain information for 6tdu d #3.72
---
Chain | Description
d | No description available
Chain information for 6tdu e #3.73
---
Chain | Description
e | No description available
Chain information for 6tdu f #3.74
---
Chain | Description
f | No description available
Chain information for 6tdu g #3.75
---
Chain | Description
g | No description available
Chain information for 6tdu h #3.76
---
Chain | Description
h | No description available
Chain information for 6tdu i #3.77
---
Chain | Description
i | No description available
Chain information for 6tdu j #3.78
---
Chain | Description
j | No description available
Chain information for 6tdu k #3.79
---
Chain | Description
k | No description available
Chain information for 6tdu l #3.80
---
Chain | Description
l | No description available
Chain information for 6tdu m #3.81
---
Chain | Description
m | No description available
Chain information for 6tdu n #3.82
---
Chain | Description
n | No description available
Chain information for 6tdu o #3.83
---
Chain | Description
o | No description available
Chain information for 6tdu p #3.84
---
Chain | Description
p | No description available
Chain information for 6tdu q #3.85
---
Chain | Description
q | No description available
Chain information for 6tdu r #3.86
---
Chain | Description
r | No description available
Chain information for 6tdu s #3.87
---
Chain | Description
s | No description available
Chain information for 6tdu t #3.88
---
Chain | Description
t | No description available
Split 6tdu (#3) into 88 models
> hide #3.1 models
> hide #!3.2 models
> show #!3.2 models
> show #3.1 models
> hide #3.15 models
> show #3.15 models
> hide #3.55 models
> show #3.55 models
> ~ribbon #3.1-54
> hide #3.56 models
> show #3.56 models
> Ribbon #3
Unknown command: Ribbon #3
> ribbon #3
> hide #3.15 models
> hide #3.40 models
> select #3/J,j,K,k,M,m,N,n
17808 atoms, 18074 bonds, 8 models selected
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel lightblue see green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel light sea green
> select clear
> select #3.83/o:105
17 atoms, 17 bonds, 1 model selected
> select up
204 atoms, 204 bonds, 1 model selected
> select up
1890 atoms, 1919 bonds, 1 model selected
> select #3.60/L:23
14 atoms, 13 bonds, 1 model selected
> select clear
> select #3.60/L:23
14 atoms, 13 bonds, 1 model selected
> select up
372 atoms, 377 bonds, 1 model selected
> select up
1008 atoms, 1025 bonds, 1 model selected
> select down
372 atoms, 377 bonds, 1 model selected
> select #3.63/O:44
22 atoms, 21 bonds, 1 model selected
> select up
343 atoms, 349 bonds, 1 model selected
> select up
1890 atoms, 1919 bonds, 1 model selected
> dssp
> select clear
> save2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> open2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/TB11_SM_EgEG7.pdb
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/su-8_SM_EgSu-8.pdb
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/su-
> e_SM_EgSu-e.pdb
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/su-
> f_SM_EgSu-f.pdb
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/su-
> g_SM_EgSu-g.pdb
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/su-
> ij_SM_EgSu-ij.pdb
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/Modeling/SwissModel/Specific_Eg_template/su-
> k_SM_EgSu-k.pdb
TB11_SM_EgEG7.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.1
[more info...]
Chain information for TB11_SM_EgEG7.pdb #4
---
Chain | Description
A | No description available
su-8_SM_EgSu-8.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.1
[more info...]
Chain information for su-8_SM_EgSu-8.pdb #5
---
Chain | Description
A | No description available
su-e_SM_EgSu-e.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.1
[more info...]
Chain information for su-e_SM_EgSu-e.pdb #6
---
Chain | Description
A | No description available
su-f_SM_EgSu-f.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.7
[more info...]
Chain information for su-f_SM_EgSu-f.pdb #7
---
Chain | Description
A | No description available
su-g_SM_EgSu-g.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.1
[more info...]
Chain information for su-g_SM_EgSu-g.pdb #8
---
Chain | Description
A | No description available
su-ij_SM_EgSu-ij.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.8
[more info...]
Chain information for su-ij_SM_EgSu-ij.pdb #9
---
Chain | Description
A | No description available
su-k_SM_EgSu-k.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 6tdu.9
[more info...]
Chain information for su-k_SM_EgSu-k.pdb #10
---
Chain | Description
A | No description available
> rename #4-10 id #4
> rename #4 SM-pairwise
> matchmaker #4.5 to #3.61
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 6tdu M, chain M (#3.61) with su-g_SM_EgSu-g.pdb, chain A (#4.5),
sequence alignment score = 179.6
RMSD between 91 pruned atom pairs is 0.311 angstroms; (across all 139 pairs:
2.661)
> hide #3.67 models
> show #3.67 models
> hide #3.87 models
> show #3.87 models
> hide #3.87 models
> show #3.87 models
> matchmaker #4.1 to #3.87
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 6tdu s, chain s (#3.87) with TB11_SM_EgEG7.pdb, chain A (#4.1),
sequence alignment score = 31.3
RMSD between 24 pruned atom pairs is 0.220 angstroms; (across all 28 pairs:
1.719)
> hide #4.1 models
> show #4.1 models
> matchmaker #4.2 to #3.80
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 6tdu l, chain l (#3.80) with su-8_SM_EgSu-8.pdb, chain A (#4.2),
sequence alignment score = 85.1
RMSD between 57 pruned atom pairs is 0.132 angstroms; (across all 57 pairs:
0.132)
> matchmaker #4.3 to #3.82
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 6tdu n, chain n (#3.82) with su-e_SM_EgSu-e.pdb, chain A (#4.3),
sequence alignment score = 92
RMSD between 55 pruned atom pairs is 0.453 angstroms; (across all 77 pairs:
5.953)
> hide #3.82 models
> show #3.82 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #4.4 models
> show #4.4 models
> hide #4.4 models
> show #4.4 models
> matchmaker #4.4 to #3.77
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 6tdu i, chain i (#3.77) with su-f_SM_EgSu-f.pdb, chain A (#4.4),
sequence alignment score = 130
RMSD between 80 pruned atom pairs is 0.278 angstroms; (across all 95 pairs:
2.051)
> hide #4.5 models
> show #4.5 models
> matchmaker #4.6 to #3.78
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 6tdu j, chain j (#3.78) with su-ij_SM_EgSu-ij.pdb, chain A (#4.6),
sequence alignment score = 120.1
RMSD between 52 pruned atom pairs is 0.217 angstroms; (across all 95 pairs:
5.976)
> matchmaker #4.7 to #3.79
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 6tdu k, chain k (#3.79) with su-k_SM_EgSu-k.pdb, chain A (#4.7),
sequence alignment score = 111.5
RMSD between 84 pruned atom pairs is 0.379 angstroms; (across all 97 pairs:
1.716)
> save2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> hide #!3 models
> show #!1 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> matchmaker #4.3 to #3.62
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 6tdu N, chain N (#3.62) with su-e_SM_EgSu-e.pdb, chain A (#4.3),
sequence alignment score = 92
RMSD between 55 pruned atom pairs is 0.457 angstroms; (across all 77 pairs:
6.024)
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> matchmaker #4.1 to #1.3
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 Tb927.3.2180_ATPTB11.pdb, chain d (#1.3) with TB11_SM_EgEG7.pdb,
chain A (#4.1), sequence alignment score = 139.1
RMSD between 8 pruned atom pairs is 1.251 angstroms; (across all 32 pairs:
6.615)
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #4.1 models
> show #4.1 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> matchmaker #4.2 to #1.6
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 Tb927.4.3450_su-8.pdb, chain f (#1.6) with su-8_SM_EgSu-8.pdb,
chain A (#4.2), sequence alignment score = 244
RMSD between 10 pruned atom pairs is 1.366 angstroms; (across all 57 pairs:
9.601)
> select #1.6/f:83
9 atoms, 8 bonds, 1 model selected
> select up
258 atoms, 263 bonds, 1 model selected
> select up
566 atoms, 590 bonds, 1 model selected
> matchmaker #4.3 to #1.12
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 Tb927.11.600_ATPTB8.pdb, chain I (#1.12) with su-e_SM_EgSu-e.pdb,
chain A (#4.3), sequence alignment score = 223
RMSD between 15 pruned atom pairs is 0.578 angstroms; (across all 61 pairs:
28.859)
> matchmaker #4.4 to #1.2
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 Tb927.3.1690_su-f.pdb, chain S (#1.2) with su-f_SM_EgSu-f.pdb,
chain A (#4.4), sequence alignment score = 390.2
RMSD between 5 pruned atom pairs is 1.260 angstroms; (across all 100 pairs:
19.862)
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> matchmaker #4.5 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tb927.2.3610_ATPTB9.pdb, chain H (#1.1) with su-g_SM_EgSu-g.pdb,
chain A (#4.5), sequence alignment score = 576
RMSD between 19 pruned atom pairs is 1.198 angstroms; (across all 127 pairs:
10.582)
> matchmaker #4.6 to #1.4
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 Tb927.3.2880_su-ij.pdb, chain a (#1.4) with su-ij_SM_EgSu-ij.pdb,
chain A (#4.6), sequence alignment score = 471.1
RMSD between 29 pruned atom pairs is 0.959 angstroms; (across all 96 pairs:
8.380)
> hide #1.4 models
> show #1.4 models
> matchmaker #4.7 to #1.10
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 Tb927.7.840_su-k.pdb, chain V (#1.10) with su-k_SM_EgSu-k.pdb,
chain A (#4.7), sequence alignment score = 400.4
RMSD between 9 pruned atom pairs is 1.170 angstroms; (across all 97 pairs:
14.521)
> matchmaker #4.3 to #3.62
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 6tdu N, chain N (#3.62) with su-e_SM_EgSu-e.pdb, chain A (#4.3),
sequence alignment score = 92
RMSD between 55 pruned atom pairs is 0.457 angstroms; (across all 77 pairs:
6.024)
> matchmaker #4.7 to #3.79
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 6tdu k, chain k (#3.79) with su-k_SM_EgSu-k.pdb, chain A (#4.7),
sequence alignment score = 111.5
RMSD between 84 pruned atom pairs is 0.379 angstroms; (across all 97 pairs:
1.716)
> matchmaker #4.6 to #3.78
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 6tdu j, chain j (#3.78) with su-ij_SM_EgSu-ij.pdb, chain A (#4.6),
sequence alignment score = 120.1
RMSD between 52 pruned atom pairs is 0.217 angstroms; (across all 95 pairs:
5.976)
> matchmaker #4.4 to #3.77
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 6tdu i, chain i (#3.77) with su-f_SM_EgSu-f.pdb, chain A (#4.4),
sequence alignment score = 130
RMSD between 80 pruned atom pairs is 0.278 angstroms; (across all 95 pairs:
2.051)
> matchmaker #4.3 to #3.82
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 6tdu n, chain n (#3.82) with su-e_SM_EgSu-e.pdb, chain A (#4.3),
sequence alignment score = 92
RMSD between 55 pruned atom pairs is 0.453 angstroms; (across all 77 pairs:
5.953)
> matchmaker #4.2 to #3.80
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 6tdu l, chain l (#3.80) with su-8_SM_EgSu-8.pdb, chain A (#4.2),
sequence alignment score = 85.1
RMSD between 57 pruned atom pairs is 0.132 angstroms; (across all 57 pairs:
0.132)
> matchmaker #4.1 to #3.87
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 6tdu s, chain s (#3.87) with TB11_SM_EgEG7.pdb, chain A (#4.1),
sequence alignment score = 31.3
RMSD between 24 pruned atom pairs is 0.220 angstroms; (across all 28 pairs:
1.719)
> matchmaker #4.3 to #3.62
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 6tdu N, chain N (#3.62) with su-e_SM_EgSu-e.pdb, chain A (#4.3),
sequence alignment score = 92
RMSD between 55 pruned atom pairs is 0.457 angstroms; (across all 77 pairs:
6.024)
> matchmaker #4.5 to #3.61
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 6tdu M, chain M (#3.61) with su-g_SM_EgSu-g.pdb, chain A (#4.5),
sequence alignment score = 179.6
RMSD between 91 pruned atom pairs is 0.311 angstroms; (across all 139 pairs:
2.661)
> hide #1.7.1 models
> show #1.7.1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> open2
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/ATPTB2_Tryp_SWISS_MOD.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/ATPTB3_Tryp_SWISS_MOd.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/ATPTB4_Tryp_SWISS_MOD.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/ATPTB_Tryp_SWISS_MOD_mod1.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/ATPTB_Tryp_SWISS_MOD_mod2.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/OSCP_Tryp_SWISS_MOD.pdb
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/c-ring_Tryp_SWISS_MOD.pdb
ATPTB2_Tryp_SWISS_MOD.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ATPTB2 [more info...]
Chain information for ATPTB2_Tryp_SWISS_MOD.pdb #5
---
Chain | Description
A | No description available
ATPTB3_Tryp_SWISS_MOd.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ATPTB3 [more info...]
Chain information for ATPTB3_Tryp_SWISS_MOd.pdb #6
---
Chain | Description
A | No description available
ATPTB4_Tryp_SWISS_MOD.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ATPTB4 [more info...]
Chain information for ATPTB4_Tryp_SWISS_MOD.pdb #7
---
Chain | Description
A | No description available
ATPTB_Tryp_SWISS_MOD_mod1.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for ATPTB_Tryp_SWISS_MOD_mod1.pdb #8
---
Chain | Description
A | No description available
ATPTB_Tryp_SWISS_MOD_mod2.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]
Chain information for ATPTB_Tryp_SWISS_MOD_mod2.pdb #9
---
Chain | Description
A | No description available
OSCP_Tryp_SWISS_MOD.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) OSCP_Euglena [more info...]
Chain information for OSCP_Tryp_SWISS_MOD.pdb #10
---
Chain | Description
A | No description available
c-ring_Tryp_SWISS_MOD.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) c-subunit [more info...]
Chain information for c-ring_Tryp_SWISS_MOD.pdb #11
---
Chain | Description
A B C D E F G H I J | No description available
> show #5-11#3.1,6,8-14,16-25,31,33-39,41-69,71-88#4.1-7#!3.2-5,7,26-30,32,70
> cartoons
> hide #5-11#3.1,6,8-14,16-25,31,33-39,41-69,71-88#4.1-7#!3.2-5,7,26-30,32,70
> atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> matchmaker #5 to #3.39
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 6tdu BM, chain BM (#3.39) with ATPTB2_Tryp_SWISS_MOD.pdb, chain A
(#5), sequence alignment score = 77
RMSD between 5 pruned atom pairs is 1.508 angstroms; (across all 166 pairs:
41.015)
> select #3.39/BM:208
10 atoms, 9 bonds, 1 model selected
> select up
201 atoms, 200 bonds, 1 model selected
> select up
3778 atoms, 3818 bonds, 1 model selected
> matchmaker #5 to #3.56
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 6tdu H, chain H (#3.56) with ATPTB2_Tryp_SWISS_MOD.pdb, chain A
(#5), sequence alignment score = 186.4
RMSD between 119 pruned atom pairs is 0.394 angstroms; (across all 147 pairs:
2.961)
> matchmaker #6 to #3.26
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 6tdu B, chain B (#3.26) with ATPTB3_Tryp_SWISS_MOd.pdb, chain A
(#6), sequence alignment score = 176.3
RMSD between 111 pruned atom pairs is 0.348 angstroms; (across all 135 pairs:
3.818)
> matchmaker #7 to #3.27
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 6tdu BA, chain BA (#3.27) with ATPTB4_Tryp_SWISS_MOD.pdb, chain A
(#7), sequence alignment score = 73.2
RMSD between 5 pruned atom pairs is 1.243 angstroms; (across all 135 pairs:
23.580)
> matchmaker #7 to #3.51
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 6tdu C, chain C (#3.51) with ATPTB4_Tryp_SWISS_MOD.pdb, chain A
(#7), sequence alignment score = 307.5
RMSD between 126 pruned atom pairs is 0.242 angstroms; (across all 135 pairs:
1.499)
> matchmaker #8 to #3.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6tdu A, chain A (#3.1) with ATPTB_Tryp_SWISS_MOD_mod1.pdb, chain A
(#8), sequence alignment score = 155.3
RMSD between 80 pruned atom pairs is 0.382 angstroms; (across all 103 pairs:
5.967)
> matchmaker #9 to #3.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6tdu A, chain A (#3.1) with ATPTB_Tryp_SWISS_MOD_mod2.pdb, chain A
(#9), sequence alignment score = 98.3
RMSD between 63 pruned atom pairs is 0.166 angstroms; (across all 69 pairs:
3.067)
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #10 models
> show #10 models
> matchmaker #10 to #3.39
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 6tdu BM, chain BM (#3.39) with OSCP_Tryp_SWISS_MOD.pdb, chain A
(#10), sequence alignment score = 468.3
RMSD between 184 pruned atom pairs is 0.284 angstroms; (across all 232 pairs:
3.425)
> matchmaker #11 to #3.16
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 6tdu AO, chain AO (#3.16) with c-ring_Tryp_SWISS_MOD.pdb, chain H
(#11), sequence alignment score = 232
RMSD between 73 pruned atom pairs is 0.596 angstroms; (across all 73 pairs:
0.596)
> matchmaker #11 to #3.41
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 6tdu BO, chain BO (#3.41) with c-ring_Tryp_SWISS_MOD.pdb, chain H
(#11), sequence alignment score = 232
RMSD between 73 pruned atom pairs is 0.593 angstroms; (across all 73 pairs:
0.593)
> open2
> /home/ondragahura/DATA/ATP_synthase/Models/Homology_models/ATPTB1_iTasser_model1.pdb
Chain information for ATPTB1_iTasser_model1.pdb #12
---
Chain | Description
A | No description available
> matchmaker #12 to #3.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6tdu A, chain A (#3.1) with ATPTB1_iTasser_model1.pdb, chain A
(#12), sequence alignment score = 307.7
RMSD between 207 pruned atom pairs is 1.003 angstroms; (across all 352 pairs:
17.832)
> rename #5-12 id #4.8-15
Invalid "id" argument: Expected an integer
> rename #5-12 id #4.8-4.15
Invalid "id" argument: Expected an integer
> save2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
> rename #5-12 id 4.8-4.15
Invalid "id" argument: Expected an integer
> rename #5-12 id 4
> rename #4.11-12 id 4.11
> rename #4.11 ATPTB1_Tryp_SWISS_MODEL
> hide #!4 models
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> save2
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
opened ChimeraX session
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #4.3 models
> show #4.3 models
> hide #4.4 models
> show #4.4 models
> open emdb:10467
Opened emd_10467.map, grid size 440,440,440, pixel 1.05, shown at level
0.0204, step 2, values float32
> select #5
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #5 level 0.02428
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #5 level 0.02849
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> lighting flat
> show #!4 models
> ~ribbon #4
> ribbon #4.8
> select #3.56/H:357
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
697 atoms, 699 bonds, 40 residues, 1 model selected
> select up
7302 atoms, 7392 bonds, 460 residues, 1 model selected
> select clear
> select #3.56/H:119
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
311 atoms, 312 bonds, 19 residues, 1 model selected
> select up
7302 atoms, 7392 bonds, 460 residues, 1 model selected
> select #3.56,76:17-267
7776 atoms, 7874 bonds, 502 residues, 2 models selected
> color sel white
> select clear
> hide #4.8 models
> ribbon #4.1
> select #3.87/s:40
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
321 atoms, 327 bonds, 18 residues, 1 model selected
> select up
1092 atoms, 1116 bonds, 65 residues, 1 model selected
> hide #4.1 models
> show #4.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select clear
> hide #4.1 models
> hide #4.2 models
> show #4.2 models
> 2ribbon #4.1
Unknown command: 2ribbon #4.1
> ribbon #4.2
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> ribbon #4.3
> hide #!3 models
> show #!3 models
> select #4.3
690 atoms, 702 bonds, 86 residues, 1 model selected
Alignment identifier is 4.3/A
> hide #4.3 models
> ribbon #4.4
> hide #4.4 models
> hide #4.5 models
> show #4.5 models
> ribbon #4.5
> dssp
> dssp energyCutoff -0.3
> dssp energyCutoff -0.2
> dssp energyCutoff -0.1
> dssp
> hide #4.5 models
> show #4.5 models
> hide #4.5 models
> ribbon #4.6
> hide #4.6 models
> ribbon #4.7
> hide #4.7 models
> show #4.7 models
> hide #4.7 models
> ribbon #4.9
> hide #4.9 models
> ribbon #4.10
> hide #4.10 models
> ribbon #4.11
> hide #!4.11 models
> ribbon #4.13
> hide #4.13 models
> ribbon #4.14
> hide #4.14 models
> ribbon #4.15
> hide #4.15 models
> show #4.15 models
> select #3.1/A:74
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
298 atoms, 301 bonds, 16 residues, 1 model selected
> select up
8684 atoms, 8779 bonds, 491 residues, 1 model selected
> show #!4.11 models
> hide #!4.11 models
> hide #4.15 models
> select clear
> lighting flat
> lighting soft
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
> save
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
opened ChimeraX session
> surface #3 color fromatoms transparency 5
Invalid "color" argument: Invalid color name or specifier
> surface #3 color fromatom transparency 5
Invalid "color" argument: Invalid color name or specifier
> surface #3 transparency 5
> select #3
271331 atoms, 274070 bonds, 43 pseudobonds, 16961 residues, 107 models
selected
> hide sel & #!3.1-14,16-39,41-88 cartoons
> show sel & #!3.1-14,16-39,41-88 cartoons
> hide sel & #!3.1-14,16-39,41-88 atoms
> hide sel & #!3.1-14,16-39,41-88 cartoons
> show sel & #!3.1-14,16-39,41-88 cartoons
> lighting soft
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> color #3 fromatoms surfaces
> save
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
opened ChimeraX session
> hide #!3.2 models
> show #!3.2 models
> hide #3.2.3 models
> rename #3.1-14,16-39,41-54,69-74 id #6
> rename #6 blues
> rename #3.58,59,61,62,78,79,81,82 id #7
> rename #7 cyans
> rename #3 whites
> save
> /home/ondragahura/Work/Publications/ATPS_Review_Parasitology/ATPS_for_review.cxs
opened ChimeraX session
> rename #3,6,7 id #8
> hide #8.2.1 models
> show #8.2.1 models
> close session
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 914, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 633, in file_close_cb
run(session, 'close session')
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2815, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/std_commands/close.py", line 60, in close_session
session.reset()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/models.py", line 570, in reset_state
self.close([m for m in self.list() if not m.SESSION_ENDURING])
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/models.py", line 888, in close
self.remove(mopen)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/models.py", line 864, in remove
del self._models[model_id]
KeyError: (8, 2, 2)
KeyError: (8, 2, 2)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/models.py", line 864, in remove
del self._models[model_id]
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 20.1.5
OpenGL renderer: Radeon RX 570 Series (POLARIS10, DRM 3.40.0, 5.4.0-51-generic, LLVM 10.0.1)
OpenGL vendor: X.Org
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 6.5Gi 21Gi 214Mi 3.5Gi 24Gi
Swap: 1.1Gi 0B 1.1Gi
Graphics:
01:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Ellesmere [Radeon RX 470/480/570/570X/580/580X/590] [1002:67df] (rev ef)
Subsystem: ASUSTeK Computer Inc. Ellesmere [Radeon RX 470/480/570/570X/580/580X/590] [1043:04c2]
Kernel driver in use: amdgpu
Locale: ('en_US', 'UTF-8')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
cftime: 1.2.1
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.8.2
ChimeraX-AtomicLibrary: 1.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202009290239
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.1
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0.1
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.2
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
netifaces: 0.10.9
networkx: 2.5
numexpr: 2.7.1
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.2.3
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.2
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.1
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → KeyError deleting models during 'close session' |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX session close error was caused by a bug in the rename command that you used to change model id numbers. That bug (#3812) was fixed on October 8, 2020. If you want to use the rename command to move a model to a lower level in the model hierarchy then you will need to use the ChimeraX daily build.
Note:
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There's a preceding 'rename' command that looks suspicious.
Reported by Ondrej Gahura.