The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA3/ranked_0.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
Unsupported scale factor (0.000000) detected on Display1
[Repeated 5 time(s)]
> rename #1 MLA3
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA8/ranked_0.pdb
Chain information for ranked_0.pdb #2
---
Chain | Description
A | No description available
B | No description available
> rename #2 MLA8
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA6/ranked_0.pdb
Chain information for ranked_0.pdb #3
---
Chain | Description
A | No description available
B | No description available
> rename #3 MLA6
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA7/ranked_0.pdb
Chain information for ranked_0.pdb #4
---
Chain | Description
A | No description available
B | No description available
> rename #4 MLA7
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA27-2/ranked_0.pdb
Chain information for ranked_0.pdb #5
---
Chain | Description
A | No description available
B | No description available
> rename #5 MLA27
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA1/ranked_0.pdb
Chain information for ranked_0.pdb #6
---
Chain | Description
A | No description available
B | No description available
> rename #6 MLA1
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA13/ranked_0.pdb
Chain information for ranked_0.pdb #7
---
Chain | Description
A | No description available
B | No description available
> rename #7 MLA13
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA18-1/ranked_0.pdb
Chain information for ranked_0.pdb #8
---
Chain | Description
A | No description available
B | No description available
> rename #8 MLA18
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA16-1/ranked_0.pdb
Chain information for ranked_0.pdb #9
---
Chain | Description
A | No description available
B | No description available
> rename #9 MLA16
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA10/ranked_0.pdb
Chain information for ranked_0.pdb #10
---
Chain | Description
A | No description available
B | No description available
> rename #10 MLA0
> ui tool show Matchmaker
> select add #1
8732 atoms, 8823 bonds, 561 residues, 1 model selected
> select add #2
17591 atoms, 17775 bonds, 1131 residues, 2 models selected
> select add #3
26308 atoms, 26578 bonds, 1690 residues, 3 models selected
> select add #4
35043 atoms, 35405 bonds, 2252 residues, 4 models selected
> select add #5
43844 atoms, 44294 bonds, 2818 residues, 5 models selected
> select add #6
52610 atoms, 53151 bonds, 3379 residues, 6 models selected
> select add #7
61351 atoms, 61981 bonds, 3941 residues, 7 models selected
> select add #8
70109 atoms, 70837 bonds, 4502 residues, 8 models selected
> select add #9
78862 atoms, 79686 bonds, 5063 residues, 9 models selected
> select add #10
87466 atoms, 88380 bonds, 5617 residues, 10 models selected
> ui tool show Matchmaker
> matchmaker #2-10 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 MLA3, chain B (#1) with MLA8, chain B (#2), sequence alignment
score = 1908.9
RMSD between 393 pruned atom pairs is 0.773 angstroms; (across all 437 pairs:
1.956)
Matchmaker MLA3, chain B (#1) with MLA6, chain B (#3), sequence alignment
score = 1839.4
RMSD between 344 pruned atom pairs is 0.954 angstroms; (across all 435 pairs:
2.703)
Matchmaker MLA3, chain B (#1) with MLA7, chain B (#4), sequence alignment
score = 1933.3
RMSD between 407 pruned atom pairs is 0.613 angstroms; (across all 436 pairs:
2.110)
Matchmaker MLA3, chain B (#1) with MLA27, chain B (#5), sequence alignment
score = 1812.9
RMSD between 390 pruned atom pairs is 0.698 angstroms; (across all 436 pairs:
2.747)
Matchmaker MLA3, chain B (#1) with MLA1, chain B (#6), sequence alignment
score = 1846.3
RMSD between 397 pruned atom pairs is 0.712 angstroms; (across all 437 pairs:
1.578)
Matchmaker MLA3, chain B (#1) with MLA13, chain B (#7), sequence alignment
score = 1973.7
RMSD between 403 pruned atom pairs is 0.656 angstroms; (across all 436 pairs:
2.410)
Matchmaker MLA3, chain B (#1) with MLA18, chain B (#8), sequence alignment
score = 1921
RMSD between 385 pruned atom pairs is 0.774 angstroms; (across all 437 pairs:
2.490)
Matchmaker MLA3, chain B (#1) with MLA16, chain B (#9), sequence alignment
score = 1901
RMSD between 389 pruned atom pairs is 0.725 angstroms; (across all 437 pairs:
2.414)
Matchmaker MLA3, chain B (#1) with MLA0, chain B (#10), sequence alignment
score = 1929.5
RMSD between 395 pruned atom pairs is 0.640 angstroms; (across all 430 pairs:
1.959)
> rename #10 MLA10
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA23/ranked_0.pdb
Chain information for ranked_0.pdb #11
---
Chain | Description
A | No description available
B | No description available
> rename #11 MLA23
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA30-1/ranked_0.pdb
Chain information for ranked_0.pdb #12
---
Chain | Description
A | No description available
B | No description available
> rename #12 MLA30
> select add #11
96068 atoms, 97072 bonds, 6172 residues, 11 models selected
> select add #12
104848 atoms, 105946 bonds, 6734 residues, 12 models selected
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA25-1/ranked_0.pdb
Chain information for ranked_0.pdb #13
---
Chain | Description
A | No description available
B | No description available
> rename #13 MLA25
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA28/ranked_0.pdb
Chain information for ranked_0.pdb #14
---
Chain | Description
A | No description available
B | No description available
> rename #14 MLA28
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA31-1/ranked_0.pdb
Chain information for ranked_0.pdb #15
---
Chain | Description
A | No description available
B | No description available
> rename #15 MLA31
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA37-1/ranked_0.pdb
Chain information for ranked_0.pdb #16
---
Chain | Description
A | No description available
B | No description available
> rename #10 MLA37
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA32/ranked_0.pdb
Chain information for ranked_0.pdb #17
---
Chain | Description
A | No description available
B | No description available
> rename #17 MLA32
> rename #10 MLA10
> rename #16 MLA37
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA35-1/ranked_0.pdb
Chain information for ranked_0.pdb #18
---
Chain | Description
A | No description available
B | No description available
> rename #18 MLA35
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA34/ranked_0.pdb
Chain information for ranked_0.pdb #19
---
Chain | Description
A | No description available
B | No description available
> rename #19 MLA34
> open /Users/gomezdd/Downloads/Pwl2_Mla_diversity_rep2/MLA12/ranked_0.pdb
Chain information for ranked_0.pdb #20
---
Chain | Description
A | No description available
B | No description available
> rename #20 MLA12
> select add #16
113463 atoms, 114653 bonds, 7287 residues, 13 models selected
> select add #17
122222 atoms, 123507 bonds, 7847 residues, 14 models selected
> select add #18
130837 atoms, 132213 bonds, 8402 residues, 15 models selected
> select add #19
139430 atoms, 140897 bonds, 8957 residues, 16 models selected
> select add #20
148276 atoms, 149832 bonds, 9521 residues, 17 models selected
> select add #15
157049 atoms, 158694 bonds, 10078 residues, 18 models selected
> select add #14
165946 atoms, 167678 bonds, 10648 residues, 19 models selected
> select add #13
174752 atoms, 176570 bonds, 11211 residues, 20 models selected
> ui tool show Matchmaker
> matchmaker #2-20 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 MLA3, chain B (#1) with MLA8, chain B (#2), sequence alignment
score = 1908.9
RMSD between 393 pruned atom pairs is 0.773 angstroms; (across all 437 pairs:
1.956)
Matchmaker MLA3, chain B (#1) with MLA6, chain B (#3), sequence alignment
score = 1839.4
RMSD between 344 pruned atom pairs is 0.954 angstroms; (across all 435 pairs:
2.703)
Matchmaker MLA3, chain B (#1) with MLA7, chain B (#4), sequence alignment
score = 1933.3
RMSD between 407 pruned atom pairs is 0.613 angstroms; (across all 436 pairs:
2.110)
Matchmaker MLA3, chain B (#1) with MLA27, chain B (#5), sequence alignment
score = 1812.9
RMSD between 390 pruned atom pairs is 0.698 angstroms; (across all 436 pairs:
2.747)
Matchmaker MLA3, chain B (#1) with MLA1, chain B (#6), sequence alignment
score = 1846.3
RMSD between 397 pruned atom pairs is 0.712 angstroms; (across all 437 pairs:
1.578)
Matchmaker MLA3, chain B (#1) with MLA13, chain B (#7), sequence alignment
score = 1973.7
RMSD between 403 pruned atom pairs is 0.656 angstroms; (across all 436 pairs:
2.410)
Matchmaker MLA3, chain B (#1) with MLA18, chain B (#8), sequence alignment
score = 1921
RMSD between 385 pruned atom pairs is 0.774 angstroms; (across all 437 pairs:
2.490)
Matchmaker MLA3, chain B (#1) with MLA16, chain B (#9), sequence alignment
score = 1901
RMSD between 389 pruned atom pairs is 0.725 angstroms; (across all 437 pairs:
2.414)
Matchmaker MLA3, chain B (#1) with MLA10, chain B (#10), sequence alignment
score = 1929.5
RMSD between 395 pruned atom pairs is 0.640 angstroms; (across all 430 pairs:
1.959)
Matchmaker MLA3, chain B (#1) with MLA23, chain B (#11), sequence alignment
score = 2087.7
RMSD between 405 pruned atom pairs is 0.598 angstroms; (across all 431 pairs:
1.315)
Matchmaker MLA3, chain B (#1) with MLA30, chain B (#12), sequence alignment
score = 1930.8
RMSD between 391 pruned atom pairs is 0.650 angstroms; (across all 436 pairs:
2.507)
Matchmaker MLA3, chain B (#1) with MLA25, chain B (#13), sequence alignment
score = 1832.8
RMSD between 393 pruned atom pairs is 0.654 angstroms; (across all 437 pairs:
1.655)
Matchmaker MLA3, chain B (#1) with MLA28, chain B (#14), sequence alignment
score = 1877.7
RMSD between 390 pruned atom pairs is 0.822 angstroms; (across all 437 pairs:
1.394)
Matchmaker MLA3, chain B (#1) with MLA31, chain B (#15), sequence alignment
score = 1757.7
RMSD between 394 pruned atom pairs is 0.623 angstroms; (across all 427 pairs:
1.894)
Matchmaker MLA3, chain B (#1) with MLA37, chain B (#16), sequence alignment
score = 1881.9
RMSD between 395 pruned atom pairs is 0.658 angstroms; (across all 429 pairs:
1.337)
Matchmaker MLA3, chain B (#1) with MLA32, chain B (#17), sequence alignment
score = 1783.1
RMSD between 372 pruned atom pairs is 0.770 angstroms; (across all 430 pairs:
2.397)
Matchmaker MLA3, chain B (#1) with MLA35, chain B (#18), sequence alignment
score = 2032.6
RMSD between 406 pruned atom pairs is 0.622 angstroms; (across all 431 pairs:
1.390)
Matchmaker MLA3, chain B (#1) with MLA34, chain B (#19), sequence alignment
score = 2010.8
RMSD between 401 pruned atom pairs is 0.502 angstroms; (across all 431 pairs:
2.151)
Matchmaker MLA3, chain B (#1) with MLA12, chain B (#20), sequence alignment
score = 1756.5
RMSD between 392 pruned atom pairs is 0.698 angstroms; (across all 436 pairs:
2.042)
*** Deleted thousands of lines to meet Trac size limit. TomG ***
> select #22/C:112
1 atom, 1 residue, 1 model selected
> display #22/C:112 :<4
> view #22/C:112 @<4
> select #22/C
175 atoms, 206 pseudobonds, 175 residues, 2 models selected
> display #22/C :<4
> view #22/C @<4
> ~select
Nothing selected
> hide #22.2 models
> select subtract #22.2
Nothing selected
> select add #22
1465 atoms, 1506 bonds, 15 pseudobonds, 187 residues, 3 models selected
> hide sel atoms
> select #22/B:93,89,27 #22/A:51
34 atoms, 30 bonds, 10 pseudobonds, 4 residues, 3 models selected
> show sel atoms
> show #!1 models
> select add #1
8766 atoms, 8853 bonds, 10 pseudobonds, 565 residues, 4 models selected
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #22/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 MLA3, chain B (#1) with PWL2_HIPP43_12-11-2020-final.pdb, chain A
(#22), sequence alignment score = 54.1
RMSD between 6 pruned atom pairs is 1.480 angstroms; (across all 64 pairs:
14.703)
> undo
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #22/B to #1/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 MLA3, chain A (#1) with PWL2_HIPP43_12-11-2020-final.pdb, chain B
(#22), sequence alignment score = 610.2
RMSD between 77 pruned atom pairs is 0.599 angstroms; (across all 112 pairs:
20.208)
> ui tool show Matchmaker
> matchmaker #!22 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 MLA3, chain B (#1) with PWL2_HIPP43_12-11-2020-final.pdb, chain A
(#22), sequence alignment score = 54.1
RMSD between 6 pruned atom pairs is 1.480 angstroms; (across all 64 pairs:
14.703)
> undo
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #!22 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 MLA3, chain A (#1) with PWL2_HIPP43_12-11-2020-final.pdb, chain B
(#22), sequence alignment score = 610.2
RMSD between 77 pruned atom pairs is 0.599 angstroms; (across all 112 pairs:
20.208)
> select #22/B:93,89,27 #22/A:51
34 atoms, 30 bonds, 10 pseudobonds, 4 residues, 3 models selected
> show sel atoms
> select #1/A:72,68,6 #1/B:405
63 atoms, 59 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/A:72,68,6 #1/B:405 #2/A:51 #2/B:93,89,27
116 atoms, 109 bonds, 8 residues, 2 models selected
> select #1/A:72,68,6 #1/B:405 #2/A:57 #2/B:93,89,27
123 atoms, 117 bonds, 8 residues, 2 models selected
> select #1/A:72,68,6 #1/B:405 #22/A:57 #22/B:93,89,27
95 atoms, 87 bonds, 10 pseudobonds, 8 residues, 3 models selected
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 22 pseudobonds, 8 residues, 4 models selected
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASN 27 OD1 no hydrogen 2.828 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B GLU 89 OE2 no hydrogen 2.848 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 93 OD1 no hydrogen 2.771 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 93 OD2 no hydrogen 3.079 N/A
8 hydrogen bonds found
4 strict hydrogen bonds found
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> ~display HC
> ~display HC, H
> hide HC, H
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display H
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> show #23 models
> color #23 #f4c600ff models
> select #22/B:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B
883 atoms, 915 bonds, 6 pseudobonds, 112 residues, 2 models selected
> show sel surfaces
> color sel byhetero
> undo
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for PWL2_HIPP43_12-11-2020-final.pdb_B SES surface #22.3:
minimum, -17.16, mean -2.53, maximum 12.28
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!22 & sel) 80
> transparency (#!22 & sel) 70
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> view sel
> hide #!1 models
> select add #22
1528 atoms, 1565 bonds, 31 pseudobonds, 191 residues, 10 models selected
> hide #22.1 models
> hide #23 models
> show #22.1 models
> show #!1 models
> hide #22.1 models
> show #22.1 models
> hide #!22 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.3 models
> show #1.3 models
> select add #1
10197 atoms, 10329 bonds, 31 pseudobonds, 748 residues, 9 models selected
> select subtract #1
1465 atoms, 1506 bonds, 15 pseudobonds, 187 residues, 6 models selected
> hide #1.1 models
> show #1.1 models
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> show #!22 models
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASN 27 OD1 no hydrogen 2.828 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B GLU 89 OE2 no hydrogen 2.848 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 93 OD1 no hydrogen 2.771 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 93 OD2 no hydrogen 3.079 N/A
8 hydrogen bonds found
4 strict hydrogen bonds found
> ~display H
> ~display HC
> show #23 models
> hide #!22.3 models
> show #22.3 models
> hide #!22.3 models
> show #22.3 models
> hide #!22.3 models
> show #22.3 models
> hide #!1 models
> show #!1 models
> hide #23 models
> hide #1.1 models
> show #1.1 models
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASN 27 OD1 no hydrogen 2.828 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B GLU 89 OE2 no hydrogen 2.848 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 93 OD1 no hydrogen 2.771 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 93 OD2 no hydrogen 3.079 N/A
8 hydrogen bonds found
4 strict hydrogen bonds found
> ~display HC
> hide #!1 models
> select add #22
1472 atoms, 1506 bonds, 15 pseudobonds, 191 residues, 8 models selected
> select subtract #22
7 atoms, 4 residues, 4 models selected
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 4 models selected
> select subtract #1
2 models selected
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 2 models selected
> select subtract #1
2 models selected
> show #!1 models
> ~display O2
> ~display O3
> ~display N2
> ~display N2+
> ~display N3+
> undo
[Repeated 4 time(s)]
> view
[Repeated 2 time(s)]
> select #1/A:72,68,6 #1/B:405 #22/A:51 #22/B:93,89,27
97 atoms, 89 bonds, 26 pseudobonds, 8 residues, 5 models selected
> view sel
> hide #!1 models
> select add #1
8766 atoms, 8853 bonds, 26 pseudobonds, 565 residues, 8 models selected
> select subtract #1
34 atoms, 30 bonds, 10 pseudobonds, 4 residues, 6 models selected
> select add #22
1465 atoms, 1506 bonds, 15 pseudobonds, 187 residues, 6 models selected
> select subtract #22
1 model selected
> show #!1 models
> hide #!22 models
> open
> /Users/gomezdd/Documents/Bioinformatics/PWL2/PWL2_structure/V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb
Chain information for V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb #21
---
Chain | Description
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #21 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 MLA3, chain A (#1) with
V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb, chain C (#21), sequence
alignment score = 612
RMSD between 78 pruned atom pairs is 0.500 angstroms; (across all 113 pairs:
22.507)
> ui tool show Matchmaker
> matchmaker #22/A to #21/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 V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb, chain B (#21) with
PWL2_HIPP43_12-11-2020-final.pdb, chain A (#22), sequence alignment score =
36.7
RMSD between 14 pruned atom pairs is 0.651 angstroms; (across all 56 pairs:
14.321)
> show #!22 models
> hide #21 models
> hide #!22 models
> select #1/B:401
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:401
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:402
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:402-403
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1/B:401
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:401
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:401-402
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #1/B:401-402
48 atoms, 47 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> transparency (#!1 & sel) 0
> coulombic sel
Coulombic values for MLA3_A SES surface #1.2: minimum, -17.07, mean -1.27,
maximum 9.94
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!1 & sel) 70
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> ~display H
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
4 hydrogen bonds found
3 strict hydrogen bonds found
> ui tool show H-Bonds
> ~display H
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
4 hydrogen bonds found
3 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 8 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
4 hydrogen bonds found
3 strict hydrogen bonds found
> ~display HC
> display HC
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> display HC
[Repeated 1 time(s)]
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> reveal HC
Unknown command: reveal HC
> select #1/A:6,68,72 #1/B:405 reveal HC
Expected a keyword
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> display HC
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 6 models selected
> select subtract #1
2 models selected
> show #!22 models
> hide #!1 models
> show #!1 models
> hide #!22 models
> select #1/B:401
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:401-402
48 atoms, 47 bonds, 2 residues, 1 model selected
> show sel cartoons
> show #!22 models
> hide #!1 models
> show #!1 models
> hide #!22.3 models
> show #22.3 models
> hide #22.1 models
> show #22.1 models
> hide #!22 models
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/mono.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 251, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/post_form.py", line 40, in
post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1285, in request
self._send_request(method, url, body, headers, encode_chunked)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1331, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1280, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1040, in _send_output
self.send(msg)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 980, in send
self.connect()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 946, in connect
self.sock = self._create_connection(
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/socket.py",
line 844, in create_connection
raise err
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/socket.py",
line 832, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 61] Connection refused
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926.png" width 3000 height 2108
> supersample 3 transparentBackground true
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> transparency (#!1 & sel) 60
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926.png" width 3000 height 2108
> supersample 3 transparentBackground true
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> display HC
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 5 restrict both interModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASN 6 OD1 MLA3 #1/B LYS 405 HZ1 2.764 1.759
MLA3 #1/B LYS 405 NZ MLA3 #1/A GLU 68 OE1 MLA3 #1/B LYS 405 HZ2 2.731 1.728
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD1 MLA3 #1/B LYS 405 HZ3 2.765 1.857
MLA3 #1/B LYS 405 NZ MLA3 #1/A ASP 72 OD2 MLA3 #1/B LYS 405 HZ3 2.867 2.059
4 hydrogen bonds found
3 strict hydrogen bonds found
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 6 models selected
> select subtract #1
2 models selected
> select #1/A:6,68,72 #1/B:405
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> view sel
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 6 models selected
> select subtract #1
2 models selected
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v1.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> show #!22 models
> hide #!1 models
> select #22/B:116
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:116-134
149 atoms, 157 bonds, 19 residues, 1 model selected
> select #22/B:101-102
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/B:101-110
70 atoms, 72 bonds, 10 residues, 1 model selected
> select #22/B:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #22/B:102-107
45 atoms, 46 bonds, 6 residues, 1 model selected
> select #22/B:103
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #22/B:103-110
54 atoms, 55 bonds, 8 residues, 1 model selected
> hide sel surfaces
> undo
> show sel surfaces
> hide sel cartoons
> hide sel surfaces
> select #22/B:101
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:101-104
33 atoms, 34 bonds, 4 residues, 1 model selected
> show sel surfaces
> select #22/B:101-102
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/B:101-110
70 atoms, 72 bonds, 10 residues, 1 model selected
> show sel surfaces
> select #22/B:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B
883 atoms, 915 bonds, 6 pseudobonds, 112 residues, 2 models selected
> coulombic sel
Coulombic values for PWL2_HIPP43_12-11-2020-final.pdb_B SES surface #22.3:
minimum, -17.16, mean -2.53, maximum 12.28
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!22 & sel) 60
> surface style #!22.3 mesh
> undo
> surface style #22 solid
> select #22/A:51 #1/B:405
31 atoms, 29 bonds, 2 residues, 2 models selected
> view sel
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> select add #1
8741 atoms, 8831 bonds, 4 pseudobonds, 562 residues, 4 models selected
> select subtract #1
9 atoms, 8 bonds, 1 residue, 3 models selected
> select subtract #22.2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #22.2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #22.2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #22.2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #22
1465 atoms, 1506 bonds, 15 pseudobonds, 187 residues, 5 models selected
> select subtract #22
1 model selected
> show #!1 models
> hide #!22 models
> show #!22 models
> hide #!1 models
> hide #!22 models
> show #!22 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #22/B to #21/C 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 V868_PWL2af2_61f18_unrelaxed_rank_1_model_2.pdb, chain C (#21) with
PWL2_HIPP43_12-11-2020-final.pdb, chain B (#22), sequence alignment score =
604.8
RMSD between 78 pruned atom pairs is 0.825 angstroms; (across all 112 pairs:
13.128)
> hide #!1 models
> show #!1 models
> hide #!22 models
> select #22/A:51 #1/B:405
31 atoms, 29 bonds, 2 residues, 2 models selected
> show #!22 models
> view sel
> hide #!22 models
> select #22/A:51 #1/B:405
31 atoms, 29 bonds, 2 residues, 2 models selected
> view sel
> graphics silhouettes false
> select add #22
1487 atoms, 1527 bonds, 15 pseudobonds, 188 residues, 5 models selected
> select subtract #22
22 atoms, 21 bonds, 1 residue, 3 models selected
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> graphics silhouettes true
> graphics silhouettes false
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v3.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> select #22/A:51 #1/B:405
31 atoms, 29 bonds, 2 residues, 2 models selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) #f6c0f9ff
> color (#!1 & sel) #ecc2f5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #f1c6faff
> color (#!1 & sel) #f6caffff
> color (#!1 & sel) #f4c9feff
> color (#!1 & sel) #c8a4cfff
> color (#!1 & sel) #a688acff
> color (#!1 & sel) #7f6984ff
> color (#!1 & sel) #635167ff
> color (#!1 & sel) #4b3e4eff
> color (#!1 & sel) #433745ff
> color (#!1 & sel) #413644ff
> color (#!1 & sel) #423644ff
> color (#!1 & sel) #483b4bff
> color (#!1 & sel) #4b3e4eff
> color (#!1 & sel) #4f4152ff
> color (#!1 & sel) #524355ff
> color (#!1 & sel) #604f64ff
> color (#!1 & sel) #715d75ff
> color (#!1 & sel) #735e77ff
> color (#!1 & sel) #76617bff
> color (#!1 & sel) #7b6580ff
> color (#!1 & sel) #826b87ff
> color (#!1 & sel) #856e8aff
> color (#!1 & sel) #89718eff
> color (#!1 & sel) #8c7391ff
> color (#!1 & sel) #907695ff
> color (#!1 & sel) #937998ff
> color (#!1 & sel) #977c9dff
> color (#!1 & sel) #9a7fa0ff
> color (#!1 & sel) #9f83a5ff
> color (#!1 & sel) #a386a9ff
> color (#!1 & sel) #a689acff
> color (#!1 & sel) #a98bb0ff
> color (#!1 & sel) #af90b5ff
> color (#!1 & sel) #b394baff
> color (#!1 & sel) #b696bdff
> color (#!1 & sel) #ba99c1ff
> color (#!1 & sel) #bb9ac2ff
> color (#!1 & sel) #bd9bc4ff
> color (#!1 & sel) #bf9dc7ff
> color (#!1 & sel) #c2a0caff
> color (#!1 & sel) #c8a5d0ff
> color (#!1 & sel) #cba7d2ff
> color (#!1 & sel) #cca8d4ff
> color (#!1 & sel) #cfaad7ff
> color (#!1 & sel) #d0abd8ff
> color (#!1 & sel) #d1acd9ff
> color (#!1 & sel) #d2addaff
[Repeated 1 time(s)]
> color (#!1 & sel) #ceaad6ff
> color (#!1 & sel) #cea9d6ff
> color (#!1 & sel) #d0abd8ff
> color (#!1 & sel) #d1acd9ff
> color (#!1 & sel) #fec7ffff
> color (#!1 & sel) #f3cafbff
> color (#!1 & sel) #f4cafcff
> color (#!1 & sel) #f7ccffff
> color (#!1 & sel) #f6cbfeff
> color (#!1 & sel) #e9c1f1ff
> color (#!1 & sel) #e1bae8ff
> color (#!1 & sel) #dbb5e2ff
> color (#!1 & sel) #d4afdbff
> color (#!1 & sel) #d0acd7ff
> color (#!1 & sel) #caa7d1ff
> color (#!1 & sel) #c7a5cdff
> color (#!1 & sel) #c6a4ccff
> color (#!1 & sel) #caa7d1ff
> color (#!1 & sel) #cdaad4ff
> color (#!1 & sel) #cfabd6ff
> color (#!1 & sel) #d0add7ff
> color (#!1 & sel) #d1add8ff
> color (#!1 & sel) #d3afdaff
> color (#!1 & sel) #d4b0dbff
> color (#!1 & sel) #d5b1dcff
> color (#!1 & sel) #cca3dcff
> color (#!1 & sel) #cda3ddff
> color (#!1 & sel) #d8ace9ff
> color (#!1 & sel) #dbafedff
> color (#!1 & sel) #dcb0eeff
> color (#!1 & sel) #dfb2f1ff
> color (#!1 & sel) #e1b3f3ff
> color (#!1 & sel) #e7b8faff
> color (#!1 & sel) #e9bafcff
> color (#!1 & sel) #ecbcffff
> color (#!1 & sel) #ebbbfdff
> color (#!1 & sel) #e5b6f7ff
> color (#!1 & sel) #e0b3f2ff
> color (#!1 & sel) #dcafeeff
> color (#!1 & sel) #d7abe8ff
> color (#!1 & sel) #d5aae7ff
> color (#!1 & sel) #d9adeaff
> color (#!1 & sel) #daaeebff
> color (#!1 & sel) #d8ace9ff
> color (#!1 & sel) #d7ace9ff
> color (#!1 & sel) #d7abe8ff
> color (#!1 & sel) #d8ace9ff
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> graphics silhouettes true
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v3.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v4.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> transparency #1 50
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v5.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v6.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> lighting soft
> graphics silhouettes false
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v7.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> transparency #1 70
> transparency #1 60
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v8.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> show #!22 models
> hide #!1 models
> select #22/B:23-24
8 atoms, 7 bonds, 2 residues, 1 model selected
> select #22/B
883 atoms, 915 bonds, 6 pseudobonds, 112 residues, 2 models selected
> coulombic sel
Coulombic values for PWL2_HIPP43_12-11-2020-final.pdb_B SES surface #22.3:
minimum, -17.16, mean -2.53, maximum 12.28
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!22 & sel) 70
> surface style #!22.3 solid
> color (#!22 & sel) cyan
> transparency (#!22 & sel) 60
> coulombic sel
Coulombic values for PWL2_HIPP43_12-11-2020-final.pdb_B SES surface #22.3:
minimum, -17.16, mean -2.53, maximum 12.28
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!22 & sel) 60
> select #22/B:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:113-134
171 atoms, 180 bonds, 22 residues, 1 model selected
> hide sel surfaces
> select #22/B:103-104
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #22/B:103-114
88 atoms, 91 bonds, 12 residues, 1 model selected
> hide sel surfaces
> select #22/B:103-104
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #22/B:103-134
241 atoms, 253 bonds, 32 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select #22/B:101-102
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/B:101-102
16 atoms, 16 bonds, 2 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> select #22/B:104
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/B:104-111
56 atoms, 57 bonds, 8 residues, 1 model selected
> select #22/B:101-102
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/B:101-110
70 atoms, 72 bonds, 10 residues, 1 model selected
> show sel surfaces
> select #22/B:101
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:101-110
70 atoms, 72 bonds, 10 residues, 1 model selected
> select #22/B:101
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:101-110
70 atoms, 72 bonds, 10 residues, 1 model selected
> select add #22
1465 atoms, 1506 bonds, 15 pseudobonds, 187 residues, 6 models selected
> select subtract #22
1 model selected
> select #22/B:111
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #22/B:111-134
187 atoms, 197 bonds, 24 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #22/B:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B
883 atoms, 915 bonds, 6 pseudobonds, 112 residues, 2 models selected
> show sel cartoons
> color (#!22 & sel) #85e5e9ff
> color (#!22 & sel) #a5e9dfff
> color (#!22 & sel) #8fe9e6ff
> color (#!22 & sel) #90eae6ff
> color (#!22 & sel) #96f4f0ff
> color (#!22 & sel) #98f7f3ff
> color (#!22 & sel) #99f8f4ff
> color (#!22 & sel) #9bfcf8ff
> color (#!22 & sel) #9dfffbff
> color (#!22 & sel) #a8f6ffff
> hide sel surfaces
> select #22/B:93,89,27
25 atoms, 22 bonds, 2 pseudobonds, 3 residues, 2 models selected
> color sel byhetero
> select #22/B
883 atoms, 915 bonds, 6 pseudobonds, 112 residues, 2 models selected
> select #22/B:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/B:110-134
196 atoms, 206 bonds, 25 residues, 1 model selected
> select #22/B:103-104
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #22/B:103-109
45 atoms, 46 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #22/B:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:120-122
16 atoms, 15 bonds, 3 residues, 1 model selected
> select #22/B:118-119
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #22/B:118-121
35 atoms, 36 bonds, 4 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select #22/B:23-24
8 atoms, 7 bonds, 2 residues, 1 model selected
> select #22/B:23-100
626 atoms, 644 bonds, 6 pseudobonds, 78 residues, 2 models selected
> show sel surfaces
> coulombic sel
Coulombic values for PWL2_HIPP43_12-11-2020-final.pdb_B SES surface #22.3:
minimum, -17.16, mean -2.53, maximum 12.28
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!22 & sel) 60
> hide #22/B
> hide #22/B cartoons
> hide #22/B surfaces
> show #!1 models
> hide #1/B cartoons
> hide #1/B atoms
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> select #1/A:6,68,72 a
Expected a keyword
> select #1/A:6,68,72 #22/A:51
50 atoms, 46 bonds, 4 pseudobonds, 4 residues, 3 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 5 restrict both intraModel false distSlop
> 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intermodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASN 6 OD1 no hydrogen 2.824 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A GLU 68 OE1 no hydrogen 3.205 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD1 no hydrogen 3.272 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD2 no hydrogen 3.320 N/A
4 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/A:6,68,72 #22/A:51
50 atoms, 46 bonds, 4 pseudobonds, 4 residues, 3 models selected
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> hide sel surfaces
> select #1/A:6,68,72 #22/A:51
50 atoms, 46 bonds, 4 pseudobonds, 4 residues, 3 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 5 restrict both intraModel false distSlop
> 0.45 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intermodel H-bonds
Constraints relaxed by 0.45 angstroms and 30 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASN 6 OD1 no hydrogen 2.824 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A GLU 68 OE1 no hydrogen 3.205 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD1 no hydrogen 3.272 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD2 no hydrogen 3.320 N/A
4 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fab02f dashes 5 restrict both intraModel false distSlop
> 0.5 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intermodel H-bonds
Constraints relaxed by 0.5 angstroms and 30 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASN 6 OD1 no hydrogen 2.824 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A GLU 68 OE1 no hydrogen 3.205 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD1 no hydrogen 3.272 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD2 no hydrogen 3.320 N/A
4 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 0.7 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intermodel H-bonds
Constraints relaxed by 0.7 angstroms and 30 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASN 6 OD1 no hydrogen 2.824 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A GLU 68 OE1 no hydrogen 3.205 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD1 no hydrogen 3.272 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A LYS 51 NZ MLA3 #1/A ASP 72 OD2 no hydrogen 3.320 N/A
4 hydrogen bonds found
0 strict hydrogen bonds found
> show #23 models
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> show sel surfaces
> select subtract #22.2
41 atoms, 38 bonds, 3 residues, 2 models selected
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP43_K51_v1.png" width 3000 height
> 2108 supersample 3 transparentBackground true
> show #11 models
> hide #!22 models
> ui tool show Matchmaker
> matchmaker #11/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 MLA3, chain B (#1) with MLA23, chain B (#11), sequence alignment
score = 2087.7
RMSD between 405 pruned atom pairs is 0.598 angstroms; (across all 431 pairs:
1.315)
> select add #11
8602 atoms, 8692 bonds, 555 residues, 1 model selected
> hide sel atoms
> show #1/B cartoons
> select add #1
17334 atoms, 17515 bonds, 4 pseudobonds, 1116 residues, 5 models selected
> select subtract #11
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 6 models selected
> select add #11
17334 atoms, 17515 bonds, 4 pseudobonds, 1116 residues, 7 models selected
> select subtract #11
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 6 models selected
> select add #11
17334 atoms, 17515 bonds, 4 pseudobonds, 1116 residues, 7 models selected
> select subtract #22.2
17334 atoms, 17515 bonds, 4 pseudobonds, 1116 residues, 7 models selected
> hide #22.1 models
> hide #23 models
> hide #22.3 models
Alignment identifier is 1
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Alignment identifier is 11/B
> show #11/B:405 atoms
> ~display HC
> show #11/B:405 atoms
> color sel byhetero
> undo
> select #11/B:405 a
Expected a keyword
> select #11/B:405
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> hide #1/B cartoons
> select #1/B
6900 atoms, 6959 bonds, 437 residues, 1 model selected
> select #11/B c
Expected a keyword
> select #11/B
6769 atoms, 6827 bonds, 431 residues, 1 model selected
> color sel #e5b7ffff
> color sel #a68bffff
> color sel #7d6fffff
> color sel #a5bcffff
> color sel #8489ffff
> color sel #9289ffff
> color sel #726bc7ff
> color sel #7b74d7ff
> color sel #9a4bd7ff
> color sel #7959d7ff
> color sel #6561d7ff
> color sel #807cd7ff
> color sel #7063d7ff
> color sel #7b6cecff
> color sel #778aecff
> color sel #9490ecff
> color sel #817dceff
> select #11/B:405
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel byhetero
> ~display HC
> ~select 11/B:405
> select subtract 11/B:405
Expected an objects specifier or a keyword
> ~select #11/B:405
Nothing selected
> select #11/B:367
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/B:367-373
102 atoms, 101 bonds, 7 residues, 1 model selected
> select #11/B:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #11/B:368-373
95 atoms, 94 bonds, 6 residues, 1 model selected
> select #11/B:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #11/B:368-371
57 atoms, 56 bonds, 4 residues, 1 model selected
> select #11/B:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #11/B:368-370
43 atoms, 42 bonds, 3 residues, 1 model selected
> hide sel cartoons
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/D926_v1.png" width 3000 height 2108
> supersample 3 transparentBackground true
> hide #11 models
> select add #11
8602 atoms, 8692 bonds, 555 residues, 1 model selected
> select subtract #11
Nothing selected
> show #6 models
> ui tool show Matchmaker
> matchmaker #6/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 MLA3, chain B (#1) with MLA1, chain B (#6), sequence alignment
score = 1846.3
RMSD between 397 pruned atom pairs is 0.712 angstroms; (across all 437 pairs:
1.578)
> select add #6
8766 atoms, 8857 bonds, 561 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> select #6/B
6933 atoms, 6992 bonds, 437 residues, 1 model selected
> color sel #ce765bff
> color sel #c975ceff
> color sel #cec856ff
> color sel #cea237ff
> color sel #ce821bff
> color sel #f0971fff
> color sel #ffa121ff
> color sel #ffc360ff
> color sel #ffce82ff
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> color sel #ffabceff
> color sel #ffc797ff
> color sel #ffab4eff
> color sel #ffaf5fff
> color sel #ffba7fff
> color sel #ffc368ff
> color sel #ffcc7fff
> color sel #ffb670ff
> ~select #6/B
Nothing selected
> show #6/B:405 atoms
> select #6/B:405 a
Expected a keyword
> select #6/B:405
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel byhetero
> ~display HC
> select add #6
8766 atoms, 8857 bonds, 561 residues, 1 model selected
Alignment identifier is 6/A
Alignment identifier is 6/B
> select #6/B:405
15 atoms, 14 bonds, 1 residue, 1 model selected
> ~select #6/B:405
Nothing selected
> select #6/B:369
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #6/B:369
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #6/B:368
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #6/B:368-369
36 atoms, 35 bonds, 2 residues, 1 model selected
> hide sel cartoons
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/E926_v1.png" width 3000 height 2108
> supersample 3 transparentBackground true
> select #1/A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> color (#!1 & sel) #b2fffbff
> transparency (#!1 & sel) 60
> ~select #1/A:6,68,72
1791 atoms, 1820 bonds, 121 residues, 2 models selected
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> select #1/A:6,68,72 a
Expected a keyword
> hide sel atoms
> show sel atoms
> color sel byhetero
> undo
> hide sel surfaces
> color sel byhetero
> show sel surfaces
> undo
[Repeated 1 time(s)]
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> hide sel surfaces
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> color sel byhetero
> ~display HC
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> show sel surfaces
> color (#!1 & sel) #b2fffbff
> transparency (#!1 & sel) 60
> ~display HC
[Repeated 1 time(s)]
> hide sel surfaces
> select up
8732 atoms, 8823 bonds, 561 residues, 2 models selected
> select up
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 4 models selected
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> color sel byhetero
> ~display HC
[Repeated 4 time(s)]
> color sel byhetero
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> ~display H
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> show sel surfaces
> color sel bychain
> undo
> coulombic sel
Coulombic values for MLA3_A SES surface #1.2: minimum, -17.07, mean -1.27,
maximum 9.94
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!1 & sel) 60
> color sel byelement
> undo
> color sel byhetero
> undo
> color (#!1 & sel) #b2fffbff
> transparency (#!1 & sel) 60
> undo
> color sel cyan target s
> transparency (#!1 & sel) 60
> color sel medium turquoise target s
> color sel turquoise target s
> color sel dark turquoise target s
> color sel aquamarine target s
> color sel sky blue target s
> color sel pale turquoise target s
> color sel dark turquoise target s
> color sel turquoise target s
> color sel medium turquoise target s
> color sel light sea green target s
> color sel cyan target s
> color sel dark turquoise target s
> color sel medium turquoise target s
> color sel dark turquoise target s
> color sel pale turquoise target s
> color sel sky blue target s
> color sel light sky blue target s
> color sel dark turquoise target s
> color sel turquoise target s
> color sel medium turquoise target s
> color sel light sea green target s
> color sel medium turquoise target s
> color sel turquoise target s
[Repeated 2 time(s)]
> color sel dark turquoise target s
> color sel cyan target s
> color sel light sea green target s
> color sel medium turquoise target s
> color sel turquoise target s
> color sel cyan target s
> color sel deep sky blue target s
[Repeated 1 time(s)]
> color sel cyan target s
> color sel turquoise target s
> color sel medium turquoise target s
> color sel dark turquoise target s
> color sel turquoise target s
> color sel cyan target s
> transparency (#!1 & sel) 60
> select subtract #22.2
1832 atoms, 1864 bonds, 124 residues, 2 models selected
> select add #22.2
1832 atoms, 1864 bonds, 124 residues, 2 models selected
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/E926_v2.png" width 3000 height 2018
> supersample 3 transparentBackground true
> hide #6 models
> show #11 models
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/D926_v2.png" width 3000 height 2018
> supersample 3 transparentBackground true
> hide #!1 models
> show #!1 models
> hide #11 models
> show #1/B
> show #1/B cartoons
[Repeated 1 time(s)]
> show #1/B:405 atoms
> ~display HC
> ~display H
> display H
> show #1/B:405 atoms
> display H
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla3_K926_v9.png" width 3000 height
> 2018 supersample 3 transparentBackground true
> show #!22 models
> hide #1/B
> hide #1/B cartoons
> show #23 models
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/HIPP43_K51_v2.png" width 3000 height
> 2018 supersample 3 transparentBackground true
> show #1/B cartoons
> hide #!22 models
> hide #1/A:6,68,72
> select #1/B:410-411
37 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/B:410-411
37 atoms, 37 bonds, 2 residues, 1 model selected
> view sel
> show sel atoms
> color sel byhetero
> ~display HC
> show #1/A:23
> select #1/A:23
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #1/A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> hide sel surfaces
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> color (#!1 & sel) cyan
> color (#!1 & sel) #8cffefff
> color (#!1 & sel) #8cfaffff
> color (#!1 & sel) #9cfff3ff
> color (#!1 & sel) #77fff7ff
> color (#!1 & sel) #5fffe7ff
> color (#!1 & sel) #a6fff6ff
> color (#!1 & sel) #beffe1ff
> color (#!1 & sel) #61ffe9ff
> color (#!1 & sel) #5bffd2ff
> color (#!1 & sel) #71ffd1ff
> color (#!1 & sel) #92ffe1ff
> color (#!1 & sel) #98fff4ff
> color (#!1 & sel) #74fff5ff
> color (#!1 & sel) #99fff5ff
> color (#!1 & sel) #a8ffecff
> color (#!1 & sel) #c3ffffff
> color (#!1 & sel) #d2fffdff
> color (#!1 & sel) #9bfeffff
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 5 models selected
> select subtract #1
2 models selected
> select #1/A:23
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/A:23
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel byhetero
> ~display HC
> select up
130 atoms, 129 bonds, 8 residues, 2 models selected
> select up
1832 atoms, 1864 bonds, 124 residues, 2 models selected
> select up
8732 atoms, 8823 bonds, 561 residues, 2 models selected
> select up
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 4 models selected
> select add #1
8732 atoms, 8823 bonds, 4 pseudobonds, 561 residues, 6 models selected
> select subtract #1
2 models selected
> select #1/A:23, #1/B:410,411
Expected an objects specifier or a keyword
> select #1/A:23 #1/B:410,411
61 atoms, 60 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 0.5 angleSlop 22.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intermodel H-bonds
Constraints relaxed by 0.5 angstroms and 22 degrees
Models used:
1 MLA3
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/A:23 #1/B:410,411
61 atoms, 60 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 0.5 angleSlop 22.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 22 degrees
Models used:
1 MLA3
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 23 N MLA3 #1/B TYR 411 O MLA3 #1/A ARG 23 H 2.889 1.906
1 hydrogen bonds found
1 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 restrict both interModel false distSlop
> 0.5 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 25 degrees
Models used:
1 MLA3
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/A:23 #1/B:410,411
61 atoms, 60 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 interModel false distSlop 0.5
> angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 25 degrees
Models used:
1 MLA3
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 23 N MLA3 #1/B TYR 411 O MLA3 #1/A ARG 23 H 2.889 1.906
MLA3 #1/A ARG 23 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
MLA3 #1/A ARG 23 NH1 MLA3 #1/B PRO 408 O MLA3 #1/A ARG 23 HH11 2.793 1.894
MLA3 #1/A ARG 23 NH2 MLA3 #1/B PRO 408 O MLA3 #1/A ARG 23 HH22 2.771 1.917
4 hydrogen bonds found
2 strict hydrogen bonds found
> select #1/A:23 #1/B:410,411
61 atoms, 60 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select #1/A:23 #1/B:410,411,408
75 atoms, 74 bonds, 4 pseudobonds, 4 residues, 2 models selected
> show sel atoms
> ~display HC
> view sel
> show #!22 models
> show #22/B cartoons
> select add #22
1540 atoms, 1580 bonds, 8 pseudobonds, 191 residues, 6 models selected
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Alignment identifier is 22/A
Alignment identifier is 22/B
> select #22/A:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/A:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/A:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/A:56-57
14 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #22/B:44
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #22/B:44
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #22/B: 44
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #22/B: 44 #22/A:56,57
25 atoms, 23 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 0.5 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 25 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> hide #23 models
> show #23 models
> show #22.2 models
> hide #22.2 models
> show #22.1 models
> hide #!1 models
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 interModel false distSlop 0.5
> angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false intraRes
> false select true reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 25 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> hide #22/A:51
> hide #22/A:51 atoms
> select #22/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/B:44 #22/A:56,57,53
33 atoms, 30 bonds, 2 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 0.5 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 25 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> ui tool show H-Bonds
> select #22/B:44 #22/A:56,57,53
33 atoms, 30 bonds, 2 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.3 dashes 5 restrict both interModel false
> distSlop 0.8 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 30 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> select #22/B:44 #22/A:56,57,53
33 atoms, 30 bonds, 2 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 1.0 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 30 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> select add #22
1465 atoms, 1506 bonds, 6 pseudobonds, 187 residues, 3 models selected
> hide #1.1 models
> hide #22.1 models
> show #22.1 models
> hide #23 models
> show #23 models
> show #11 models
> hide #!22 models
> show #!1 models
> hide #1/B #11/A
> hide #1/B cartoons #11/A c
Expected ',' or a keyword
> hide #1/B c , #11/A c
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> hide #1/B cartoons
> hide #1/B atoms
> hide #11/B:405 atoms
> hide #11/B:410,411 atoms
> show #11/B:410,411 atoms
[Repeated 1 time(s)]
> select #11/B:410,411
31 atoms, 32 bonds, 2 residues, 1 model selected
> select add #11
8602 atoms, 8692 bonds, 555 residues, 1 model selected
Alignment identifier is 11/A
Alignment identifier is 11/B
> show #11/B:410,411 atoms
> select #11/B:410,411
31 atoms, 32 bonds, 2 residues, 1 model selected
> color sel byhetero
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!22 models
> hide #!1 models
> show #!1 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #11/A
> hide #11/A atoms
[Repeated 1 time(s)]
> hide #11/A cartoons
[Repeated 1 time(s)]
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla23_Pwl2.pdb" displayedOnly true
> select #11/B #1/A
8601 atoms, 8691 bonds, 555 residues, 2 models selected
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla23_Pwl2.pdb" selectedOnly true
> hide sel atoms
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla23_Pwl2.pdb" models #1,11
> selectedOnly true
[Repeated 1 time(s)]
> combine #11/B #1/A modelID 24 name MLA23_PWL2
Expected a keyword
> combine #11/B #1/A modelID #24 name MLA23_PWL2
Expected a keyword
> combine #11/B, #1/A modelID #24 name MLA23_PWL2
Expected a keyword
> select #11/B #1/A
8601 atoms, 8691 bonds, 555 residues, 2 models selected
> combine #11/B #1/A
Remapping chain ID 'A' in MLA3 #1 to 'C'
Remapping chain ID 'B' in MLA3 #1 to 'D'
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #23 models
> hide #!1 models
> hide #11 models
> select #24
17334 atoms, 17515 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla23_Pwl2.pdb" models #24
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla23_Pwl2.pdb" models #24
> displayedOnly true
> select subtract #22.2
17334 atoms, 17515 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> hide #22.1 models
> hide #1.2 models
> hide #1.3 models
Alignment identifier is 1
Alignment identifier is 24/B
Alignment identifier is 24/D
> remove #24/D
Unknown command: remove #24/D
> delete #24/D
> delete #24/C
> show #24/A
Undo failed, probably because structures have been modified.
> delete #24
> show #!1 models
> hide #!1 models
> show #!1 models
> show #11 models
> combine #11/B #1/A
Remapping chain ID 'A' in MLA3 #1 to 'C'
Remapping chain ID 'B' in MLA3 #1 to 'D'
> delete #24/D
> select add #24
10434 atoms, 10556 bonds, 679 residues, 1 model selected
Alignment identifier is 1
Alignment identifier is 24/B
> delete #24/A
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/Mla23_Pwl2.pdb" models #24
> rename #24 MLA23_PWL2
> show #24/B:410,411 atoms
> select #24/B:410,411
31 atoms, 32 bonds, 2 residues, 1 model selected
> view sel
> select #24/C:23
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #24/C:23
24 atoms, 23 bonds, 1 residue, 1 model selected
> show #24/a:23 atoms
> show #24/A:23 atoms
> show #24/C:23 atoms
> hide #!1 models
> show #!1 models
> show #1/B
> show #1/B cartoons
> show #1/B:410,411 atoms
> ~display HC
> show #14 models
> hide #14 atoms
> hide #14/A
> ui tool show Matchmaker
> matchmaker #14/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 MLA3, chain B (#1) with MLA28, chain B (#14), sequence alignment
score = 1877.7
RMSD between 390 pruned atom pairs is 0.822 angstroms; (across all 437 pairs:
1.394)
> show #14/B:410,411
> ~display HC
> hide #11 models
> hide #!24 models
> ~display H
> show #!24 models
> show #3 models
> hide #3/B atoms
> hide #3/B atoms #3/A b
Expected ',' or a keyword
> hide #3/B atoms #3/A a
Expected ',' or a keyword
> hide #3 atoms
> hide #3/A
> ui tool show Matchmaker
> matchmaker #3/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 MLA3, chain B (#1) with MLA6, chain B (#3), sequence alignment
score = 1839.4
RMSD between 344 pruned atom pairs is 0.954 angstroms; (across all 435 pairs:
2.703)
> select #3/A c
Expected a keyword
> select #3/A
1833 atoms, 1865 bonds, 124 residues, 1 model selected
> select #3/b
6884 atoms, 6938 bonds, 435 residues, 1 model selected
> color sel purple
> color sel #ceb9ffff
> color sel #44ff50ff
> color sel #72ff72ff
> color sel #c5ff86ff
> color sel #ffcdeeff
> color sel #ffb1b3ff
> color sel #ff5178ff
> color sel #d44363ff
> color sel #c03d5aff
> color sel #c0687bff
> color sel #c04865ff
> color sel #c02b54ff
> color sel #881e3bff
> color sel #9d2344ff
> color sel #9d4f58ff
> color sel #9d483aff
> color sel #9d2126ff
> color sel #9d2643ff
> select #3/b:410,411
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #3/b:410,411
43 atoms, 42 bonds, 2 residues, 1 model selected
> show atoms
> select #3/b:410,411
43 atoms, 42 bonds, 2 residues, 1 model selected
> show #3/B:410,411 atoms
> hide #3/B:410,411 atoms
> show #3/B:408,409 atoms
> select #3/B:408,409
36 atoms, 36 bonds, 2 residues, 1 model selected
> color sel byhetero
> ~display HC
> ~display H
> color #14 #734c87ff
> color #14 #9663b0ff
> color #14 #d089f4ff
> color #14 #7c5292ff
> color #14 #863692ff
> select #14/B:410,411
41 atoms, 41 bonds, 2 residues, 1 model selected
> color sel byhetero
> show #!22 models
> show #1.1 models
> hide #!22 models
> hide #!24 models
> hide #14 models
> hide #3 models
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> show #!22 models
> hide #!22 models
> select #1/A:23
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:23 #1/B:410,411
61 atoms, 60 bonds, 2 pseudobonds, 3 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 1.0 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 30 degrees
Models used:
1 MLA3
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 23 N MLA3 #1/B TYR 411 O MLA3 #1/A ARG 23 H 2.889 1.906
MLA3 #1/A ARG 23 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
MLA3 #1/A ARG 23 NH1 MLA3 #1/B TYR 411 OH MLA3 #1/A ARG 23 HH12 4.157 3.535
3 hydrogen bonds found
1 strict hydrogen bonds found
> ~display H
> ~display HC
> show #!22 models
> show #23 models
> hide #23 models
> select subtract #22.2
6 atoms, 3 residues, 3 models selected
> show #22.3 models
> hide #22.3 models
> select #22/B:44 #22/A:56,57
25 atoms, 23 bonds, 2 pseudobonds, 3 residues, 2 models selected
> hide #!1 models
> select #22/B:44 #22/A:56,57
25 atoms, 23 bonds, 2 pseudobonds, 3 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 1.0 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 30 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> hide #24.1 models
> select subtract #24.1
4 atoms, 3 residues, 2 models selected
> select add #22
1465 atoms, 1506 bonds, 2 pseudobonds, 187 residues, 3 models selected
Alignment identifier is 22/A
Alignment identifier is 22/B
> select #22/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #22/B:44 #22/A:56,57
25 atoms, 23 bonds, 2 pseudobonds, 3 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 1.0 angleSlop 35.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 35 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> select #22/B:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/B:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/B:44,48 #22/A:56,57
34 atoms, 31 bonds, 2 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 1.0 angleSlop 30.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 30 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 OG1 PWL2_HIPP43_12-11-2020-final.pdb #22/B GLU 48 O no hydrogen 2.846 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
3 hydrogen bonds found
2 strict hydrogen bonds found
> show #!1 models
> select #22/B:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/B:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> color sel byhetero
> select #1/B:376
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> hide #1/B:376
> hide #2/B:48
> hide #22/B:48
> hide #22/A53
> hide #22/A:53
> select #22/A:56,57
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #22/A:56,57 #22/B:44
25 atoms, 23 bonds, 2 pseudobonds, 3 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 1.0 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 1 angstroms and 25 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N PWL2_HIPP43_12-11-2020-final.pdb #22/A THR 57 O no hydrogen 2.834 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> select #22/A:56,57 #22/B:44
25 atoms, 23 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select #1/A:23 #1/B:410,411
61 atoms, 60 bonds, 3 pseudobonds, 3 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both interModel false
> distSlop 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 23 N MLA3 #1/B TYR 411 O MLA3 #1/A ARG 23 H 2.889 1.906
MLA3 #1/A ARG 23 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
2 hydrogen bonds found
1 strict hydrogen bonds found
> select #22/B:44 #1/B:410,411
48 atoms, 47 bonds, 3 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #fab02f radius 0.1 dashes 5 restrict both intraModel false
> distSlop 0.45 angleSlop 25.0 twoColors true slopColor #f7bb22 intraMol false
> intraRes false select true reveal true retainCurrent true log true
Finding intermodel H-bonds
Constraints relaxed by 0.45 angstroms and 25 degrees
Models used:
1 MLA3
22 PWL2_HIPP43_12-11-2020-final.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 N MLA3 #1/B TYR 411 O no hydrogen 2.641 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) MLA3 #1/B VAL 410 O no hydrogen 2.800 N/A
2 hydrogen bonds found
1 strict hydrogen bonds found
> hide #1/A #22/B
> hide #1/A #22/A
> hide #1/A #22/A cartoons
> hide #1/A #22/A atoms
> show #23 models
> select add #1
8734 atoms, 8823 bonds, 2 pseudobonds, 562 residues, 5 models selected
Alignment identifier is 1/A
Alignment identifier is 1/B
Destroying pre-existing alignment with identifier 22/B
Alignment identifier is 22/B
> save "/Users/gomezdd/OneDrive - Norwich BioScience
> Institutes/Mla3_mimicry/Figure_mimicry/MLAs.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 624, in take_snapshot
data = {'structure': self.structure,
File "atomic_cpp/cymol.pyx", line 1562, in
chimerax.atomic.cymol.CyResidue.structure.__get__
RuntimeError: Residue already deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>
ValueError: error processing: 'tools' -> -> -> : Error while saving session
data for 'tools' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac14,7
Model Number: MNEJ3B/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 16 days, 27 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PL2492H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
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: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Looks like CheckWaterViewer kept a reference to a deleted water that prevented session save from working.
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fbbc8754220> -> <chimerax.check_waters.tool.CheckWaterViewer object at
0x7fbb98dea8b0> -> <chimerax.atomic.molobject.Residue object at
0x7fbbdd68cd80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fbbc8754220> ->
<chimerax.check_waters.tool.CheckWaterViewer object at 0x7fbb98dea8b0> ->
<chimerax.atomic.molobject.Residue object at 0x7fbbdd68cd80>