MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

[stefan.knight@…]

The following bug report has been submitted:
Platform:        Darwin-20.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Selecting chains. Using Matchmaker.  Only started happening after 9th pdb loaded, with one molecule having been deleted earlier.

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/stefan/Dropbox/MdTMPK manuscript/5nrn_dimer.pdb" format pdb

5nrn_dimer.pdb title:  
MTB TMK crystal structure In complex with compound 3 [more info...]  
  
Chain information for 5nrn_dimer.pdb #1  
---  
Chain | Description  
A B | thymidylate kinase  
  
Non-standard residues in 5nrn_dimer.pdb #1  
---  
95W —
5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione  
CL — chloride ion  
  

> hide atoms

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open /Users/stefan/Dropbox/MdTMPK/Refine_209/MdTMPK_refine_209.pdb format
> pdb

Summary of feedback from opening
/Users/stefan/Dropbox/MdTMPK/Refine_209/MdTMPK_refine_209.pdb  
---  
warning | Ignored bad PDB record found on line 61  
  
Chain information for MdTMPK_refine_209.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> select clear

> select clear

> select clear

> hide atoms

> mmaker #2 to #1 showAlignment true

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 5nrn_dimer.pdb, chain B (#1) with MdTMPK_refine_209.pdb, chain A
(#2), sequence alignment score = 305.9  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 5nrn_dimer.pdb #1/B,
MdTMPK_refine_209.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 99 pruned atom pairs is 0.930 angstroms; (across all 192 pairs:
4.791)  
  

> select #2/B

3011 atoms, 3035 bonds, 2 pseudobonds, 199 residues, 2 models selected  

> select add #2/D

4801 atoms, 4835 bonds, 10 pseudobonds, 319 residues, 2 models selected  

> hide sel cartoons

> select clear

> select clear

> open "/Users/stefan/Dropbox/MdTMPK manuscript/3ld9_dimer.pdb"

3ld9_dimer.pdb title:  
Crystal structure of thymidylate kinase from ehrlichia chaffeensis At 2.15A
resolution [more info...]  
  
Chain information for 3ld9_dimer.pdb #3  
---  
Chain | Description  
A B C D | DTMP kinase  
  
Non-standard residues in 3ld9_dimer.pdb #3  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
SO4 — sulfate ion  
  

> mmaker #3 to #1 showAlignment true

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 5nrn_dimer.pdb, chain A (#1) with 3ld9_dimer.pdb, chain A (#3),
sequence alignment score = 237.3  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 5nrn_dimer.pdb #1/A,
3ld9_dimer.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 90 pruned atom pairs is 1.105 angstroms; (across all 171 pairs:
4.005)  
  

> select clear

> select add #3/A

1543 atoms, 1496 bonds, 2 pseudobonds, 261 residues, 2 models selected  

> select clear

> select add #3/C

1397 atoms, 1375 bonds, 4 pseudobonds, 221 residues, 2 models selected  

> select add #3/D

2969 atoms, 2875 bonds, 8 pseudobonds, 504 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select

19377 atoms, 19023 bonds, 36 pseudobonds, 2384 residues, 6 models selected  

> hide sel atoms

> select clear

> ui tool show Matchmaker

> matchmaker #!3 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 5nrn_dimer.pdb, chain B (#1) with 3ld9_dimer.pdb, chain A (#3),
sequence alignment score = 236  
RMSD between 90 pruned atom pairs is 1.064 angstroms; (across all 172 pairs:
4.184)  
  

> ui mousemode right zoom

> ui tool show Contacts

> open "/Users/stefan/Dropbox/MdTMPK manuscript/2plr.pdb"

2plr.pdb title:  
Crystal structure of DTMP kinase (ST1543) from sulfolobus tokodaii STRAIN7
[more info...]  
  
Chain information for 2plr.pdb #4  
---  
Chain | Description  
A B | DTMP kinase  
  
Non-standard residues in 2plr.pdb #4  
---  
1PE — pentaethylene glycol (PEG400)  
CL — chloride ion  
DTT — 2,3-dihydroxy-1,4-dithiobutane (1,4-dithiothreitol)  
EDO — 1,2-ethanediol (ethylene glycol)  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
PEG — di(hydroxyethyl)ether  
PG4 — tetraethylene glycol  
PGE — triethylene glycol  
PO4 — phosphate ion  
  

> select

23547 atoms, 22717 bonds, 38 pseudobonds, 3354 residues, 8 models selected  

> hide sel atoms

> select clear

> matchmaker #!4 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 5nrn_dimer.pdb, chain B (#1) with 2plr.pdb, chain A (#4), sequence
alignment score = 249.4  
RMSD between 94 pruned atom pairs is 1.263 angstroms; (across all 187 pairs:
4.757)  
  

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> hide sel cartoons

> select

23547 atoms, 22717 bonds, 38 pseudobonds, 3354 residues, 8 models selected  

> hide sel cartoons

> select add #2/A

23547 atoms, 22717 bonds, 38 pseudobonds, 3354 residues, 8 models selected  

> select add #2/C

23547 atoms, 22717 bonds, 38 pseudobonds, 3354 residues, 8 models selected  

> show sel cartoons

> select clear

> select

23547 atoms, 22717 bonds, 38 pseudobonds, 3354 residues, 8 models selected  

> hide sel cartoons

> select clear

> select clear

> select add #2/A

3032 atoms, 3057 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> select add #2/C

5201 atoms, 5241 bonds, 10 pseudobonds, 345 residues, 2 models selected  

> show sel cartoons

> select clear

Drag select of 345 residues, 10 pseudobonds  

> hide sel cartoons

> select clear

> select add #3/A

1543 atoms, 1496 bonds, 2 pseudobonds, 261 residues, 2 models selected  

> select add #3/B

3060 atoms, 2951 bonds, 6 pseudobonds, 527 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select add #3/A

1543 atoms, 1496 bonds, 2 pseudobonds, 261 residues, 2 models selected  

> select add #3/B

3060 atoms, 2951 bonds, 6 pseudobonds, 527 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select add #4/A

5235 atoms, 4840 bonds, 6 pseudobonds, 1064 residues, 3 models selected  

> select add #4/B

7230 atoms, 6645 bonds, 8 pseudobonds, 1497 residues, 4 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select add #4/A

2175 atoms, 1889 bonds, 537 residues, 1 model selected  

> select add #4/B

4170 atoms, 3694 bonds, 2 pseudobonds, 970 residues, 2 models selected  

> show sel cartoons

> select add #1/A#1/B

7474 atoms, 6771 bonds, 4 pseudobonds, 1657 residues, 4 models selected  

> show sel cartoons

> select clear

> select add #2/A

3032 atoms, 3057 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> select add #2/C

5201 atoms, 5241 bonds, 10 pseudobonds, 345 residues, 2 models selected  

> select add #3/A

6744 atoms, 6737 bonds, 12 pseudobonds, 606 residues, 4 models selected  

> select add #3/B

8261 atoms, 8192 bonds, 16 pseudobonds, 872 residues, 4 models selected  

> select add #4/A

10436 atoms, 10081 bonds, 16 pseudobonds, 1409 residues, 5 models selected  

> select add #4/B

12431 atoms, 11886 bonds, 18 pseudobonds, 1842 residues, 6 models selected  

> select add #1/A#1/B

15735 atoms, 14963 bonds, 20 pseudobonds, 2529 residues, 8 models selected  

> show sel cartoons

> select clear

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> hide sel cartoons

> open "/Users/stefan/Dropbox/MdTMPK manuscript/5uiv.pdb"

5uiv.pdb title:  
Structure of thymidylate kinase from candida albicans reveals origin of broad
substrate specificity and A novel structural element. [more info...]  
  
Chain information for 5uiv.pdb #5  
---  
Chain | Description  
A | bifunctional thymidylate/uridylate kinase  
  
Non-standard residues in 5uiv.pdb #5  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
TMP — thymidine-5'-phosphate  
  
Drag select of 189 atoms, 225 residues, 11 pseudobonds, 159 bonds  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

Drag select of 1130 residues, 18 pseudobonds  

> hide sel cartoons

> select clear

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select add #2/A

6336 atoms, 6134 bonds, 4 pseudobonds, 887 residues, 4 models selected  

> select add #2/C

8505 atoms, 8318 bonds, 12 pseudobonds, 1032 residues, 4 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select add #3/A

1543 atoms, 1496 bonds, 2 pseudobonds, 261 residues, 2 models selected  

> select add #3/B

3060 atoms, 2951 bonds, 6 pseudobonds, 527 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> hide sel atoms

> hide sel cartoons

> select clear

> select add #4/A

2175 atoms, 1889 bonds, 537 residues, 1 model selected  

> select add #4/B

4170 atoms, 3694 bonds, 2 pseudobonds, 970 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> show sel cartoons

> select clear

> open "/Users/stefan/Dropbox/MdTMPK manuscript/1p6x.pdb"

1p6x.pdb title:  
Crystal structure of EHV4-TK complexed with thy and SO4 [more info...]  
  
Chain information for 1p6x.pdb #6  
---  
Chain | Description  
A B | thymidine kinase  
  
Non-standard residues in 1p6x.pdb #6  
---  
SO4 — sulfate ion  
THM — thymidine (deoxythymidine; 2'-deoxythymidine)  
  
Drag select of 334 atoms, 662 residues, 276 bonds  

> hide sel atoms

> select clear

> matchmaker #6 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 5nrn_dimer.pdb, chain B (#1) with 1p6x.pdb, chain B (#6), sequence
alignment score = 215  
RMSD between 39 pruned atom pairs is 1.047 angstroms; (across all 194 pairs:
13.411)  
  

> select clear

> select add #2/A

3032 atoms, 3057 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> show sel cartoons

> select add #2/C

5201 atoms, 5241 bonds, 10 pseudobonds, 345 residues, 2 models selected  

> show sel cartoons

> select clear

> select add #2/A

3032 atoms, 3057 bonds, 2 pseudobonds, 200 residues, 2 models selected  

> hide sel cartoons

> select add #2/C

5201 atoms, 5241 bonds, 10 pseudobonds, 345 residues, 2 models selected  

> hide sel cartoons

Drag select of 1062 residues, 2 pseudobonds  

> hide sel cartoons

> select clear

> open "/Users/stefan/Dropbox/MdTMPK manuscript/1mrn.pdb"

1mrn.pdb title:  
Crystal structure of mycobacterium tuberculosis thymidylate kinase complexed
with bisubstrate inhibitor (TP5A) [more info...]  
  
Chain information for 1mrn.pdb #7  
---  
Chain | Description  
A | thymidylate kinase  
  
Non-standard residues in 1mrn.pdb #7  
---  
MG — magnesium ion  
SO4 — sulfate ion  
T5A — P1-(5'-adenosyl)P5-(5'-thymidyl)pentaphosphate  
  
Associated 1mrn.pdb chain A to 5nrn_dimer.pdb, chain B with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: 5nrn_dimer.pdb #1/B,
MdTMPK_refine_209.pdb #2/A, 1mrn.pdb #7/A  
Associated 1mrn.pdb chain A to 5nrn_dimer.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 2: 5nrn_dimer.pdb #1/A,
3ld9_dimer.pdb #3/A, 1mrn.pdb #7/A  

> delete #7

Chains used in RMSD evaluation for alignment 1: 5nrn_dimer.pdb #1/B,
MdTMPK_refine_209.pdb #2/A  
Chains used in RMSD evaluation for alignment 2: 5nrn_dimer.pdb #1/A,
3ld9_dimer.pdb #3/A  

> select add #1/A#1/B

3304 atoms, 3077 bonds, 2 pseudobonds, 687 residues, 2 models selected  

> show sel cartoons

> select clear

Drag select of 398 residues, 2 pseudobonds  

> hide sel cartoons

> select clear

> select add #3/A

1543 atoms, 1496 bonds, 2 pseudobonds, 261 residues, 2 models selected  

> select add #3/B

3060 atoms, 2951 bonds, 6 pseudobonds, 527 residues, 2 models selected  

> select add #4/A

5235 atoms, 4840 bonds, 6 pseudobonds, 1064 residues, 3 models selected  

> select add #4/B

7230 atoms, 6645 bonds, 8 pseudobonds, 1497 residues, 4 models selected  

> show sel cartoons

> open "/Users/stefan/Dropbox/MdTMPK manuscript/2cck_dimer.pdb"

2cck_dimer.pdb title:  
Crystal structure of unliganded S. Aureus thymidylate kinase [more info...]  
  
Chain information for 2cck_dimer.pdb #7  
---  
Chain | Description  
A B | DTMP kinase  
  
Non-standard residues in 2cck_dimer.pdb #7  
---  
CL — chloride ion  
EDO — 1,2-ethanediol  
  

> matchmaker #!7 to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 3ld9_dimer.pdb, chain A (#3) with 2cck_dimer.pdb, chain B (#7),
sequence alignment score = 466.5  
RMSD between 127 pruned atom pairs is 1.048 angstroms; (across all 174 pairs:
2.942)  
  

> select clear

> open "/Users/stefan/Dropbox/MdTMPK manuscript/2wwf_dimer.pdb"

2wwf_dimer.pdb title:  
Plasmodium falciparum thymidylate kinase In complex with TMP and adp [more
info...]  
  
Chain information for 2wwf_dimer.pdb #8  
---  
Chain | Description  
A B C | thymidilate kinase, putative  
  
Non-standard residues in 2wwf_dimer.pdb #8  
---  
ADP — adenosine-5'-diphosphate  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NA — sodium ion  
TMP — thymidine-5'-phosphate  
  

> matchmaker #!8 to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 3ld9_dimer.pdb, chain A (#3) with 2wwf_dimer.pdb, chain A (#8),
sequence alignment score = 309.9  
RMSD between 117 pruned atom pairs is 0.921 angstroms; (across all 173 pairs:
2.944)  
  

> matchmaker #8/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 5nrn_dimer.pdb, chain B (#1) with 2wwf_dimer.pdb, chain B (#8),
sequence alignment score = 284.5  
RMSD between 109 pruned atom pairs is 1.035 angstroms; (across all 187 pairs:
3.969)  
  

> matchmaker #8/C to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 5nrn_dimer.pdb, chain B (#1) with 2wwf_dimer.pdb, chain C (#8),
sequence alignment score = 283.3  
RMSD between 108 pruned atom pairs is 1.078 angstroms; (across all 187 pairs:
4.667)  
  

> matchmaker #8/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 5nrn_dimer.pdb, chain B (#1) with 2wwf_dimer.pdb, chain B (#8),
sequence alignment score = 284.5  
RMSD between 109 pruned atom pairs is 1.035 angstroms; (across all 187 pairs:
3.969)  
  
Drag select of 1800 residues, 58 pseudobonds, 873 atoms, 711 bonds  

> hide sel atoms

> select clear

> select add #8/A

2021 atoms, 1862 bonds, 16 pseudobonds, 418 residues, 2 models selected  

> hide sel cartoons

> open "/Users/stefan/Dropbox/MdTMPK manuscript/3v9p.pdb"

3v9p.pdb title:  
Crystal structure of thymidylate kinase from burkholderia thailandensis [more
info...]  
  
Chain information for 3v9p.pdb #9  
---  
Chain | Description  
A B | DTMP kinase  
  
Non-standard residues in 3v9p.pdb #9  
---  
ACT — acetate ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MRD — (4R)-2-methylpentane-2,4-diol  
PEG — di(hydroxyethyl)ether  
  

> matchmaker #!9 to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 3ld9_dimer.pdb, chain A (#3) with 3v9p.pdb, chain A (#9), sequence
alignment score = 523.9  
RMSD between 120 pruned atom pairs is 0.853 angstroms; (across all 174 pairs:
2.511)  
  

> matchmaker #9/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 5nrn_dimer.pdb, chain B (#1) with 3v9p.pdb, chain B (#9), sequence
alignment score = 271.2  
RMSD between 70 pruned atom pairs is 1.017 angstroms; (across all 191 pairs:
8.205)  
  

> matchmaker #9/A to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 5nrn_dimer.pdb, chain B (#1) with 3v9p.pdb, chain A (#9), sequence
alignment score = 276.6  
RMSD between 71 pruned atom pairs is 0.999 angstroms; (across all 188 pairs:
7.898)  
  
Drag select of 1990 residues, 26 pseudobonds, 181 atoms, 146 bonds  

> hide sel atoms

> select clear

> matchmaker #9/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 3ld9_dimer.pdb, chain A (#3) with 3v9p.pdb, chain A (#9), sequence
alignment score = 523.9  
RMSD between 120 pruned atom pairs is 0.853 angstroms; (across all 174 pairs:
2.511)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> matchmaker #9/B to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 3ld9_dimer.pdb, chain A (#3) with 3v9p.pdb, chain B (#9), sequence
alignment score = 523.9  
RMSD between 121 pruned atom pairs is 0.896 angstroms; (across all 174 pairs:
2.485)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select add #9/A

1694 atoms, 1596 bonds, 4 pseudobonds, 328 residues, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select clear

> select add #9/A

1694 atoms, 1596 bonds, 4 pseudobonds, 328 residues, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select add #9/B

3415 atoms, 3211 bonds, 6 pseudobonds, 668 residues, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select add #2/A

6447 atoms, 6268 bonds, 8 pseudobonds, 868 residues, 4 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.1.12
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3,1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      System Firmware Version: 426.0.0.0.0
      SMC Version (system): 2.32f21

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 8 days 16:29

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 4096 x 2304 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 58C231756C929
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    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: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 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: 2.0
    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
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    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
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    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: 1.2.3
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[pett]

Hi Stefan,

Thanks for reporting this problem. I _believe_ it is fixed in the current daily build. Sorry for the annoyance.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab