Crash after running MatchMaker

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.4.dev202112080557 (2021-12-08 05:57:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x0000c438 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00009f84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-packages\chimerax\ui\gui.py", line 316 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202112080557\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open C:\Users\lylst\Desktop\PDB\6npy.pdb format pdb

6npy.pdb title:  
Cryo-em structure of NLRP3 bound to NEK7 [more info...]  
  
Chain information for 6npy.pdb #1  
---  
Chain | Description | UniProt  
A | nacht, LRR and pyd domains-containing protein 3 | NLRP3_HUMAN  
B | protein kinase R,serine/threonine-protein kinase NEK7 | NEK7_HUMAN  
  
Non-standard residues in 6npy.pdb #1  
---  
ADP — adenosine-5'-diphosphate  
  

> select /B

1359 atoms, 1394 bonds, 2 pseudobonds, 167 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> open C:/Users/lylst/Desktop/PDB/4kxf.pdb

4kxf.pdb title:  
Crystal structure of NLRC4 reveals its autoinhibition mechanism [more info...]  
  
Chain information for 4kxf.pdb #2  
---  
Chain | Description | UniProt  
B | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
D | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
F | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
H | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
K | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
L | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
N | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
P | NLR family card domain-containing protein 4 | NLRC4_MOUSE  
  
Non-standard residues in 4kxf.pdb #2  
---  
ADP — adenosine-5'-diphosphate  
SO4 — sulfate ion  
  

> hide #!1 models

> view

> select #1/A

6219 atoms, 6336 bonds, 7 pseudobonds, 799 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #2

57081 atoms, 58156 bonds, 26 pseudobonds, 7155 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #2/B

7236 atoms, 7374 bonds, 2 pseudobonds, 905 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/F

7199 atoms, 7336 bonds, 2 pseudobonds, 900 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/H

7162 atoms, 7296 bonds, 4 pseudobonds, 899 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/K

7235 atoms, 7372 bonds, 3 pseudobonds, 905 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/L

7134 atoms, 7270 bonds, 4 pseudobonds, 894 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/N

7028 atoms, 7158 bonds, 5 pseudobonds, 884 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/P

6883 atoms, 7009 bonds, 4 pseudobonds, 867 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> preset cartoons/nucleotides ribbons/slabs

Changed 7177 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui tool show "Color Actions"

> set bgColor light gray

> open C:/Users/lylst/Desktop/PDB/6j5u.pdb

6j5u.pdb title:  
Ligand-triggered allosteric adp release primes A plant NLR complex [more
info...]  
  
Chain information for 6j5u.pdb #3  
---  
Chain | Description | UniProt  
A | disease resistance RPP13-like protein 4 | R13L4_ARATH  
B | protein kinase superfamily protein | Q9SVY5_ARATH  
C | probable serine/threonine-protein kinase PBL2 | PBL2_ARATH  
  
Non-standard residues in 6j5u.pdb #3  
---  
BQL — [(2~{S})-2-azanyl-3-oxidanylidene-propyl]
[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
hydrogenphosphate  
BQO — [(2~{R},3~{S})-3-azanyl-4-oxidanylidene-
butan-2-yl][(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylhydrogen
phosphate  
  

> hide #!2 models

> view

> hide #!3 models

> open C:/Users/lylst/Desktop/PDB/6j5w.pdb

6j5w.pdb title:  
Ligand-triggered allosteric adp release primes A plant NLR complex [more
info...]  
  
Chain information for 6j5w.pdb #4  
---  
Chain | Description | UniProt  
A | disease resistance RPP13-like protein 4 | R13L4_ARATH  
B | RKS1 | U5LSK3_ARATH  
  
Non-standard residues in 6j5w.pdb #4  
---  
ADP — adenosine-5'-diphosphate  
  

> select #4/B

2455 atoms, 2501 bonds, 1 pseudobond, 306 residues, 2 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> select #3/A

5266 atoms, 5365 bonds, 3 pseudobonds, 663 residues, 2 models selected  

> select #4/A

6530 atoms, 6653 bonds, 1 pseudobond, 817 residues, 2 models selected  

> select #3/A

5266 atoms, 5365 bonds, 3 pseudobonds, 663 residues, 2 models selected  

> select #3/A

5266 atoms, 5365 bonds, 3 pseudobonds, 663 residues, 2 models selected  

> hide #!4 atoms

> undo

> view sel

> hide #!4 models

> select #3

9288 atoms, 9471 bonds, 8 pseudobonds, 1164 residues, 2 models selected  

> show #!1 models

> cofr sel

> view sel

> help help:user

> ui tool show Matchmaker

> matchmaker #!2,4 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 6npy.pdb, chain A (#1) with 4kxf.pdb, chain D (#2), sequence
alignment score = 552.9  
RMSD between 155 pruned atom pairs is 1.166 angstroms; (across all 728 pairs:
31.416)  
  
Matchmaker 6npy.pdb, chain A (#1) with 6j5w.pdb, chain A (#4), sequence
alignment score = 277.8  
RMSD between 39 pruned atom pairs is 1.220 angstroms; (across all 633 pairs:
38.654)  
  

> show #!3 models

> show #!4 models

> ~select #3

Nothing selected  

> hide #!4 models

> show #!2 models

> ui tool show Matchmaker

> matchmaker #!2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6npy.pdb, chain A (#1) with 4kxf.pdb, chain D (#2), sequence
alignment score = 552.9  
RMSD between 155 pruned atom pairs is 1.166 angstroms; (across all 728 pairs:
31.416)  
  
Matchmaker 6npy.pdb, chain A (#1) with 6j5u.pdb, chain A (#3), sequence
alignment score = 219.7  
RMSD between 30 pruned atom pairs is 1.186 angstroms; (across all 520 pairs:
32.901)  
  

> matchmaker #!2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6npy.pdb, chain A (#1) with 4kxf.pdb, chain D (#2), sequence
alignment score = 552.9  
RMSD between 155 pruned atom pairs is 1.166 angstroms; (across all 728 pairs:
31.416)  
  
Matchmaker 6npy.pdb, chain A (#1) with 6j5u.pdb, chain A (#3), sequence
alignment score = 219.7  
RMSD between 30 pruned atom pairs is 1.186 angstroms; (across all 520 pairs:
32.901)  
  

> hide #!3 models

> view

> hide #!2 models

> show #!3 models

> sequence chain #4/A

Alignment identifier is 4/A  

> select #3/C

1393 atoms, 1423 bonds, 4 pseudobonds, 174 residues, 2 models selected  

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> select #3/B

2629 atoms, 2683 bonds, 1 pseudobond, 327 residues, 2 models selected  

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> ui tool show Matchmaker

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6npy.pdb, chain A (#1) with 6j5u.pdb, chain A (#3), sequence
alignment score = 219.7  
RMSD between 30 pruned atom pairs is 1.186 angstroms; (across all 520 pairs:
32.901)  
  

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6npy.pdb, chain A (#1) with 6j5u.pdb, chain A (#3), sequence
alignment score = 219.7  
RMSD between 30 pruned atom pairs is 1.186 angstroms; (across all 520 pairs:
32.901)  
  

> matchmaker #!3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6npy.pdb, chain A (#1) with 6j5u.pdb, chain A (#3), sequence
alignment score = 219.7  
RMSD between 30 pruned atom pairs is 1.186 angstroms; (across all 520 pairs:
32.901)  
  

> view

> hide #!1 models

> hide #!3 models

> open C:/Users/lylst/Desktop/PDB/3jbl.pdb

3jbl.pdb title:  
Cryo-em structure of the activated NAIP2/NLRC4 inflammasome reveals nucleated
polymerization [more info...]  
  
Chain information for 3jbl.pdb #5  
---  
Chain | Description | UniProt  
A B C D E F G H I J K | NLR family card domain-containing protein 4 |
NLRC4_MOUSE  
  

> preset cartoons/nucleotides ribbons/slabs

Changed 80124 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select #2/D

7204 atoms, 7341 bonds, 2 pseudobonds, 901 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #5/A

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/C

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/D

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/E

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/F

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/G

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/H

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/I

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/J

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select #5/K

7284 atoms, 7423 bonds, 1 pseudobond, 909 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> view

> show #!1 models

> show #!2 models

> ui tool show Matchmaker

> matchmaker #!1-2 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3jbl.pdb, chain B (#5) with 6npy.pdb, chain A (#1), sequence
alignment score = 569.8  
RMSD between 11 pruned atom pairs is 1.097 angstroms; (across all 734 pairs:
24.730)  
  
Matchmaker 3jbl.pdb, chain B (#5) with 4kxf.pdb, chain D (#2), sequence
alignment score = 4131.5  
RMSD between 202 pruned atom pairs is 1.303 angstroms; (across all 900 pairs:
21.787)  
  

> hide #!1 models

> hide #!2 models

> hide #!5 models

> open "C:/Users/lylst/Desktop/PDB/未确认 210518.crdownload"

Unrecognized file suffix '.crdownload'  

> open C:/Users/lylst/Desktop/PDB/6j5t.pdb

6j5t.pdb title:  
Reconstitution and structure of A plant NLR resistosome conferring immunity
[more info...]  
  
Chain information for 6j5t.pdb #6  
---  
Chain | Description | UniProt  
A D I J M | probable serine/threonine-protein kinase PBL2 | PBL2_ARATH  
B E H K N | protein kinase superfamily protein | Q9SVY5_ARATH  
C F G L O | disease resistance RPP13-like protein 4 | R13L4_ARATH  
  
Non-standard residues in 6j5t.pdb #6  
---  
BQL — [(2~{S})-2-azanyl-3-oxidanylidene-propyl]
[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
hydrogenphosphate  
BQO — [(2~{R},3~{S})-3-azanyl-4-oxidanylidene-
butan-2-yl][(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylhydrogen
phosphate  
DTP — 2'-deoxyadenosine 5'-triphosphate  
  

> preset cartoons/nucleotides ribbons/slabs

Changed 53338 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select #6/A#6/D#6/I#6/J#6/M

7813 atoms, 7983 bonds, 15 pseudobonds, 975 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> select #6/B#6/E#6/H#6/K#6/N

13145 atoms, 13415 bonds, 5 pseudobonds, 1635 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> select #6/C

6506 atoms, 6628 bonds, 2 pseudobonds, 809 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> select #6/F

6506 atoms, 6628 bonds, 2 pseudobonds, 809 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> select #6/G

6506 atoms, 6628 bonds, 2 pseudobonds, 809 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> select #6/L

6506 atoms, 6628 bonds, 2 pseudobonds, 809 residues, 2 models selected  

> delete atoms (#!6 & sel)

> delete bonds (#!6 & sel)

> view

> show #!3 models

> ui tool show Matchmaker

> matchmaker #!3 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6j5t.pdb, chain O (#6) with 6j5u.pdb, chain A (#3), sequence
alignment score = 2712.7  
RMSD between 431 pruned atom pairs is 0.961 angstroms; (across all 659 pairs:
18.456)  
  

> matchmaker #!3 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6j5t.pdb, chain O (#6) with 6j5u.pdb, chain A (#3), sequence
alignment score = 2712.7  
RMSD between 431 pruned atom pairs is 0.961 angstroms; (across all 659 pairs:
18.456)  
  

> view

> hide #!3 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!1 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6j5t.pdb, chain O (#6) with 6npy.pdb, chain A (#1), sequence
alignment score = 284.2  
RMSD between 42 pruned atom pairs is 0.980 angstroms; (across all 645 pairs:
27.322)  
  

> view

> ui tool show Matchmaker

> matchmaker #!6 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 6npy.pdb, chain A (#1) with 6j5t.pdb, chain O (#6), sequence
alignment score = 284.2  
RMSD between 42 pruned atom pairs is 0.980 angstroms; (across all 645 pairs:
27.322)  
  

> matchmaker #!6 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 6npy.pdb, chain A (#1) with 6j5t.pdb, chain O (#6), sequence
alignment score = 284.2  
RMSD between 42 pruned atom pairs is 0.980 angstroms; (across all 645 pairs:
27.322)  
  

> matchmaker #!6 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 6npy.pdb, chain A (#1) with 6j5t.pdb, chain O (#6), sequence
alignment score = 284.2  
RMSD between 42 pruned atom pairs is 0.980 angstroms; (across all 645 pairs:
27.322)  
  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4.dev202112080557 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.14822 Core Profile Forward-Compatible Context 20.50.26.03 27.20.15026.3004
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: LENOVO
Model: 20YN
OS: Microsoft Windows 10 家庭中文版 (Build 19042)
Memory: 14,888,198,144
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31.5
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202112080557
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.15.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1