![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8167 closed defect (fixed)
Matchmaker behavior changed
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
matchmaker behaviour has changed in v1.5. In 1.4 the following commands result in the beta-barrels all aligning together. In 1.5, chain B from model #2 is aligning to #1. This is despite the matchmaker command specifically saying to align chain A from #2.
Commands:
close session
# Open models
# lateral-closed "zipped"
open 4N75
# lateral-closed "kinked"
open 5ayw
# lateral-open
open 5ljo
# lateral-open (extreme)
open 6V05
hide #1,2,3,4 targ ac
show #1,2,3,4/A:422-810 targ c
mmaker #2/A:600-end to #1
mmaker #3/A:600-end to #1
mmaker #4/A:600-end to #1
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7ojf
Summary of feedback from opening 7ojf fetched from pdb
---
notes | Fetching compressed mmCIF 7ojf from
http://files.rcsb.org/download/7ojf.cif
Fetching CCD PLM from http://ligand-expo.rcsb.org/reports/P/PLM/PLM.cif
Fetching CCD L8Z from http://ligand-expo.rcsb.org/reports/L/L8Z/L8Z.cif
Fetching CCD LPP from http://ligand-expo.rcsb.org/reports/L/LPP/LPP.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
7ojf title:
Cryo-em structure of SLYB13-bama from escherichia coli [more info...]
Chain information for 7ojf #1
---
Chain | Description | UniProt
A B C D E F G H I J K L M | Outer membrane lipoprotein slyB | D2AGE2_SHIF2
N | Outer membrane protein assembly factor BamA | C3TPJ2_ECOLX
Non-standard residues in 7ojf #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
L8Z —
(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-
oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-
oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid
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)
PLM — palmitic acid
> hide atoms
> show cartoons
> lighting soft
> set bgColor white
> set bgColor black
> close session
> open 4C4V
Summary of feedback from opening 4C4V fetched from pdb
---
note | Fetching compressed mmCIF 4c4v from
http://files.rcsb.org/download/4c4v.cif
4c4v title:
Structure of the outer membrane protein insertase BamA with one POTRA domain.
[more info...]
Chain information for 4c4v #1
---
Chain | Description | UniProt
A | OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA | BAMA_ECOLI
B | OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA | BAMA_ECOLI
4c4v mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 4K3B
Summary of feedback from opening 4K3B fetched from pdb
---
note | Fetching compressed mmCIF 4k3b from
http://files.rcsb.org/download/4k3b.cif
4k3b title:
The crystal structure of BamA from Neisseria gonorrhoeae [more info...]
Chain information for 4k3b #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | Q5F5W8_NEIG1
> mmaker #2/A 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 4c4v, chain A (#1) with 4k3b, chain A (#2), sequence alignment
score = 909.4
RMSD between 243 pruned atom pairs is 1.128 angstroms; (across all 419 pairs:
16.584)
> lighting simple
> open 4K3C
Summary of feedback from opening 4K3C fetched from pdb
---
note | Fetching compressed mmCIF 4k3c from
http://files.rcsb.org/download/4k3c.cif
4k3c title:
The crystal structure of BamA from Haemophilus ducreyi lacking POTRA domains
1-3 [more info...]
Chain information for 4k3c #3
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | Q93PM2_HAEDC
> mmaker #3/A 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 4c4v, chain A (#1) with 4k3c, chain A (#3), sequence alignment
score = 1355.4
RMSD between 317 pruned atom pairs is 0.899 angstroms; (across all 438 pairs:
8.805)
> hide #!1 models
> hide #!2 models
> hide #3 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #3 models
> hide #3 models
> hide #!2 models
> open 4N75
Summary of feedback from opening 4N75 fetched from pdb
---
note | Fetching compressed mmCIF 4n75 from
http://files.rcsb.org/download/4n75.cif
4n75 title:
Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis [more
info...]
Chain information for 4n75 #4
---
Chain | Description | UniProt
A B | Outer membrane protein assembly factor BamA | BAMA_ECOLI
4n75 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #4/A 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 4c4v, chain A (#1) with 4n75, chain A (#4), sequence alignment
score = 1930
RMSD between 339 pruned atom pairs is 0.632 angstroms; (across all 360 pairs:
1.377)
> show #3 models
> hide #3 models
> fetch 5OR1
Unknown command: fetch 5OR1
> open 5OR1
Summary of feedback from opening 5OR1 fetched from pdb
---
note | Fetching compressed mmCIF 5or1 from
http://files.rcsb.org/download/5or1.cif
5or1 title:
BamA structure of Salmonella enterica [more info...]
Chain information for 5or1 #5
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_SALTY
> mmaker #5/A 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 4c4v, chain A (#1) with 5or1, chain A (#5), sequence alignment
score = 1978.2
RMSD between 329 pruned atom pairs is 0.742 angstroms; (across all 362 pairs:
1.962)
> hide #!4 models
> open 6LYU
Summary of feedback from opening 6LYU fetched from pdb
---
note | Fetching compressed mmCIF 6lyu from
http://files.rcsb.org/download/6lyu.cif
6lyu title:
Structure of the BAM complex [more info...]
Chain information for 6lyu #6
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> hide #5#!6 atoms
> show #5#!6 cartoons
> dssp
> open emdb:30018
Summary of feedback from opening 30018 fetched from emdb
---
note | Fetching compressed map 30018 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30018/map/emd_30018.map.gz
Opened emdb 30018 as #7, grid size 296,296,296, pixel 1, shown at level
0.00324, step 2, values float32
> volume #7 step 1
> volume #7 level 0.008292
> volume #7 level 0.01174
> transparency 50
> close session
[Repeated 1 time(s)]
> open 4N75
4n75 title:
Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis [more
info...]
Chain information for 4n75 #1
---
Chain | Description | UniProt
A B | Outer membrane protein assembly factor BamA | BAMA_ECOLI
4n75 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 5ayw
5ayw title:
Structure of a membrane complex [more info...]
Chain information for 5ayw #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #3
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 6V05
6v05 title:
Cryo-EM structure of a substrate-engaged Bam complex [more info...]
Chain information for 6v05 #4
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | W8SZY2_ECOLX
D | Outer membrane protein assembly factor BamD | A0A0H3MJ38_ECO7I
E | Outer membrane protein assembly factor BamE | A0A3S5E0E0_ECOLX
F | Outer membrane protein assembly factor BamA,Outer membrane protein
assembly factor BamA,Outer membrane protein assembly factor BamA,Outer
membrane protein assembly factor BamA | BAMA_ECOLI
> hide #1,2,3,4 target a
> show #1,2,3,4/A:422-810 target c
> mmaker #2/A:600-end 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> mmaker #3/A:600-end 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 4n75, chain A (#1) with 5ljo, chain A (#3), sequence alignment
score = 1072.6
RMSD between 162 pruned atom pairs is 0.956 angstroms; (across all 201 pairs:
1.715)
> mmaker #4/A:600-end 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 4n75, chain A (#1) with 6v05, chain A (#4), sequence alignment
score = 931.7
RMSD between 162 pruned atom pairs is 0.768 angstroms; (across all 180 pairs:
1.850)
> color #1,2,3,4/A rgb(0.252,0.680,1.000)
> color #1,2,3,4/B rgb(0.000,0.831,0.321)
> color #1,2,3,4/C rgb(1.000,0.861,0.137)
> color #1,2,3,4/D rgb(1.000,0.400,0.100)
> color #1,2,3,4/E rgb(0.780,0.000,0.400)
> hide #1,2,3,4 target ac
> show #1,2,3,4/A:422-810 target c
> close session
> open 4N75
4n75 title:
Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis [more
info...]
Chain information for 4n75 #1
---
Chain | Description | UniProt
A B | Outer membrane protein assembly factor BamA | BAMA_ECOLI
4n75 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 5ayw
5ayw title:
Structure of a membrane complex [more info...]
Chain information for 5ayw #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #3
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 6V05
6v05 title:
Cryo-EM structure of a substrate-engaged Bam complex [more info...]
Chain information for 6v05 #4
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | W8SZY2_ECOLX
D | Outer membrane protein assembly factor BamD | A0A0H3MJ38_ECO7I
E | Outer membrane protein assembly factor BamE | A0A3S5E0E0_ECOLX
F | Outer membrane protein assembly factor BamA,Outer membrane protein
assembly factor BamA,Outer membrane protein assembly factor BamA,Outer
membrane protein assembly factor BamA | BAMA_ECOLI
> hide #1,2,3,4 target ac
> show #1,2,3,4/A:422-810 target c
> mmaker #2/A:600-end 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> mmaker #3/A:600-end 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 4n75, chain A (#1) with 5ljo, chain A (#3), sequence alignment
score = 1072.6
RMSD between 162 pruned atom pairs is 0.956 angstroms; (across all 201 pairs:
1.715)
> mmaker #4/A:600-end 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 4n75, chain A (#1) with 6v05, chain A (#4), sequence alignment
score = 931.7
RMSD between 162 pruned atom pairs is 0.768 angstroms; (across all 180 pairs:
1.850)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> mmaker #2/A:600-end 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> mmaker #2/A:600-810 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> mmaker #2/A:600-810 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> mmaker #2\A:600-810 to #1
> matchmaker #2\A:600-810 to #1
Missing or invalid "matchAtoms" argument: only initial part "#2" of atom
specifier valid
> mmaker #2/A:600-810 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> hide #3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:275
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:275-636
2867 atoms, 2933 bonds, 362 residues, 1 model selected
> select #2/A:693
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:232-693
3637 atoms, 3723 bonds, 462 residues, 1 model selected
> select #2/A:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A
6133 atoms, 6271 bonds, 1 pseudobond, 785 residues, 2 models selected
> close session
> open 4N75
4n75 title:
Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis [more
info...]
Chain information for 4n75 #1
---
Chain | Description | UniProt
A B | Outer membrane protein assembly factor BamA | BAMA_ECOLI
4n75 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 5ayw
5ayw title:
Structure of a membrane complex [more info...]
Chain information for 5ayw #2
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECOLI
E | Outer membrane protein assembly factor BamE | BAME_ECOLI
> open 5ljo
Summary of feedback from opening 5ljo fetched from pdb
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
5ljo title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for 5ljo #3
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI
D | Outer membrane protein assembly factor BamD | BAMD_ECO57
E | Outer membrane protein assembly factor BamE | BAME_ECOL6
> open 6V05
6v05 title:
Cryo-EM structure of a substrate-engaged Bam complex [more info...]
Chain information for 6v05 #4
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECOLI
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI
C | Outer membrane protein assembly factor BamC | W8SZY2_ECOLX
D | Outer membrane protein assembly factor BamD | A0A0H3MJ38_ECO7I
E | Outer membrane protein assembly factor BamE | A0A3S5E0E0_ECOLX
F | Outer membrane protein assembly factor BamA,Outer membrane protein
assembly factor BamA,Outer membrane protein assembly factor BamA,Outer
membrane protein assembly factor BamA | BAMA_ECOLI
> mmaker #2/A:600-end 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1070.1
RMSD between 181 pruned atom pairs is 0.573 angstroms; (across all 194 pairs:
1.136)
> hide atoms
> show cartoons
> mmaker #2/A 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 4n75, chain B (#1) with 5ayw, chain A (#2), sequence alignment
score = 1973
RMSD between 353 pruned atom pairs is 0.614 angstroms; (across all 368 pairs:
0.984)
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)
OS Loader Version: 540.120.3~19
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 2:48
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 555X:
Chipset Model: Radeon Pro 555X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00e3
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501P-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2417H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 5K9YD73MC82L
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (4)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Comparison |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Matchmaker behavior changed |
comment:2 by , 3 years ago
Hi Samuel,
Thanks for providing the all the details necessary to reproduce this behavior, that was very helpful.
Though you specify matching chain A from model #2 ro #1, you don't specify what chain of #1 to match to. #1 has both A and B chains. The command now matches #2/A to #1/B. To guarantee the matching you want you need to use #1/A in your command.
The scoring for matching model 2's chain A to #1's A and B chains is very similar, and apparently changed between versions 1.4 and 1.5. The scoring in 1.4 was 1051.5 and 1031.7 respectively, whereas in 1.5 it is 1051.5 and 1070.1 respectively. I will investigate the cause for the scoring difference, but a change this small could well be due to other bug fixes/tweaks to other parts of the code.
Even if this turns out to be a bug, it is safer in the long term for your script to explicitly specify #1/A in its matching commands. I will update this ticket with what I find from investigating the scoring change.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:3 by , 3 years ago
Okay, this is a minor bug in that matchmaker is using the structure's originally assigned secondary structure for some of the chain pairings (rather than secondary structure it computes itself). Am working on a fix.
comment:4 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Okay, this is fixed now and your script will work the same as 1.4 in tomorrow's daily build. Nonetheless, still wisest to use the explicit #1/A.
--Eric
fix: https://github.com/RBVI/ChimeraX/commit/557bb204d9add041df8161a35881143fbeedf66d
Note:
See TracTickets
for help on using tickets.
Reported by Samuel Haysom