Opened 3 years ago

Closed 3 years ago

#8167 closed defect (fixed)

Matchmaker behavior changed

Reported by: bssfh@… Owned by: pett
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 pett, 3 years ago

Cc: Elaine Meng added
Component: Unassigned → Structure Comparison
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Matchmaker behavior changed

Reported by Samuel Haysom

comment:2 by pett, 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 pett, 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 pett, 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

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