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Opened 20 months ago
Last modified 20 months ago
#15041 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (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)
> select subtract #2
165893 atoms, 167618 bonds, 10641 residues, 19 models selected
> select subtract #3
157176 atoms, 158815 bonds, 10082 residues, 18 models selected
> select subtract #4
148441 atoms, 149988 bonds, 9520 residues, 17 models selected
> select subtract #5
139640 atoms, 141099 bonds, 8954 residues, 16 models selected
> select subtract #6
130874 atoms, 132242 bonds, 8393 residues, 15 models selected
> select subtract #7
122133 atoms, 123412 bonds, 7831 residues, 14 models selected
> select subtract #8
113375 atoms, 114556 bonds, 7270 residues, 13 models selected
> select subtract #9
104622 atoms, 105707 bonds, 6709 residues, 12 models selected
> select add #2
113481 atoms, 114659 bonds, 7279 residues, 13 models selected
> select subtract #10
104877 atoms, 105965 bonds, 6725 residues, 12 models selected
> select subtract #11
96275 atoms, 97273 bonds, 6170 residues, 11 models selected
> select subtract #12
87495 atoms, 88399 bonds, 5608 residues, 10 models selected
> select subtract #13
78689 atoms, 79507 bonds, 5045 residues, 9 models selected
> select subtract #14
69792 atoms, 70523 bonds, 4475 residues, 8 models selected
> select subtract #15
61019 atoms, 61661 bonds, 3918 residues, 7 models selected
> select subtract #16
52404 atoms, 52954 bonds, 3365 residues, 6 models selected
> select subtract #17
43645 atoms, 44100 bonds, 2805 residues, 5 models selected
> select subtract #18
35030 atoms, 35394 bonds, 2250 residues, 4 models selected
> select subtract #19
26437 atoms, 26710 bonds, 1695 residues, 3 models selected
> select subtract #20
17591 atoms, 17775 bonds, 1131 residues, 2 models selected
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #19 models
> hide #20 models
> hide #18 models
> hide #17 models
> hide #16 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #2/A
> hide #2/A:
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2/A
> hide MLA8/A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide MLA8
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2
> hide #2/a cartoons
> hide #2 models
> show #2 models
Alignment identifier is 1
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Alignment identifier is 2/B
> hide #2 models
> select #1/B cartoon
Expected a keyword
> select #1/B
6900 atoms, 6959 bonds, 437 residues, 1 model selected
> color sel #ffb4e5ff
> color sel #ef98ffff
> color sel #eaacffff
> color sel #d48fffff
> color sel #f28cffff
> color sel #ff96f3ff
> color sel #fdc0ffff
> color sel #bc8fbeff
> color sel #d6a3d8ff
> color sel #d785d8ff
> color sel #d895c8ff
> color sel #b57da8ff
> color sel #c88abaff
> color sel #da96caff
> color sel #d88cdaff
> color sel #d8a5daff
> color sel #b78cb8ff
> color sel #c798c9ff
> lighting flat
> lighting soft
> color sel #dba7dcff
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> lighting flat
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> color sel #95dcc8ff
> color sel #a3d7dcff
> color sel #a9d6dcff
> color sel #b7e7efff
> color sel #a6efdcff
> color sel #8befe1ff
> color sel #a7efe7ff
> color sel #b3efecff
> color sel #acdbefff
> color sel #9ae4efff
> color sel #a5f3feff
> select #1/B:405,410,411
59 atoms, 58 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.45 angleSlop 22.0
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 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
> select #1/B:405,410,411
59 atoms, 58 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 22.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 22 degrees
Models used:
1 MLA3
5 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/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
5 hydrogen bonds found
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/B:405,410,411
59 atoms, 58 bonds, 3 residues, 1 model selected
> open
> /Users/gomezdd/Downloads/PWL2_cb1e6/PWL2_cb1e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
PWL2_cb1e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #21
---
Chain | Description
A | No description available
B | 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 B (#1) with
PWL2_cb1e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#21), sequence alignment score = 2169.9
RMSD between 420 pruned atom pairs is 0.541 angstroms; (across all 430 pairs:
0.749)
> select add #21
4170 atoms, 4250 bonds, 525 residues, 2 models selected
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Alignment identifier is 21/A
Alignment identifier is 21/B
> select subtract #21
59 atoms, 58 bonds, 3 residues, 1 model selected
> select #21/B:403
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #21/B:403
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 22.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 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
> ui tool show Contacts
> contacts sel resSeparation 5 interModel false intraMol false select true
> reveal true
No atoms match given atom specifier
> open
> /Users/gomezdd/Documents/Bioinformatics/PWL2/PWL2_structure/PWL2_HIPP43_12-11-2020-final.pdb
PWL2_HIPP43_12-11-2020-final.pdb title:
\--- [more info...]
Chain information for PWL2_HIPP43_12-11-2020-final.pdb #22
---
Chain | Description
A | No description available
B | No description available
> 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)
Alignment identifier is 2
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Destroying pre-existing alignment with identifier 2/B
Alignment identifier is 2/B
Alignment identifier is 3/B
Alignment identifier is 4/B
Alignment identifier is 5/B
Alignment identifier is 6/B
Alignment identifier is 7/B
Alignment identifier is 8/B
Alignment identifier is 9/B
Alignment identifier is 10/B
Alignment identifier is 11/B
Alignment identifier is 12/B
Alignment identifier is 13/B
Alignment identifier is 14/B
Alignment identifier is 15/B
Alignment identifier is 16/B
Alignment identifier is 17/B
Alignment identifier is 18/B
Alignment identifier is 19/B
Alignment identifier is 20/B
Destroying pre-existing alignment with identifier 21/A
Alignment identifier is 21/A
Destroying pre-existing alignment with identifier 21/B
Alignment identifier is 21/B
Alignment identifier is 22/A
Alignment identifier is 22/B
> view
> select #22/A:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/A:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/A:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> view sel
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 22.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 22 degrees
Models used:
22 PWL2_HIPP43_12-11-2020-final.pdb
1 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 NE (alt loc B) PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 56 O no hydrogen 3.289 N/A
1 hydrogen bonds found
> ui tool show "Side View"
> view sel
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> ui tool show H-Bonds
> hbonds sel intraModel false distSlop 0.45 angleSlop 22.0 intraMol false
> intraRes false select true reveal true log true
Finding intermodel H-bonds
Constraints relaxed by 0.45 angstroms and 22 degrees
Models used:
1 MLA3
2 MLA8
3 MLA6
4 MLA7
5 MLA27
6 MLA1
7 MLA13
8 MLA18
9 MLA16
10 MLA10
11 MLA23
12 MLA30
13 MLA25
14 MLA28
15 MLA31
16 MLA37
17 MLA32
18 MLA35
19 MLA34
20 MLA12
21 PWL2_cb1e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
22 PWL2_HIPP43_12-11-2020-final.pdb
14 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/B VAL 410 N MLA8 #2/B HIS 407 O MLA3 #1/B VAL 410 H 2.906 1.999
MLA3 #1/B VAL 410 N MLA27 #5/B HIS 406 O MLA3 #1/B VAL 410 H 3.093 2.124
MLA3 #1/B VAL 410 N MLA1 #6/B HIS 407 O MLA3 #1/B VAL 410 H 3.230 2.279
MLA3 #1/B VAL 410 N MLA13 #7/B HIS 406 O MLA3 #1/B VAL 410 H 2.847 1.898
MLA3 #1/B VAL 410 N MLA18 #8/B HIS 407 O MLA3 #1/B VAL 410 H 2.879 1.991
MLA3 #1/B VAL 410 N MLA16 #9/B HIS 407 O MLA3 #1/B VAL 410 H 3.425 2.461
MLA3 #1/B VAL 410 N MLA10 #10/B HIS 406 O MLA3 #1/B VAL 410 H 3.366 2.408
MLA3 #1/B VAL 410 N MLA25 #13/B HIS 407 O MLA3 #1/B VAL 410 H 3.476 2.552
MLA3 #1/B VAL 410 N MLA31 #15/B HIS 401 O MLA3 #1/B VAL 410 H 3.026 2.153
MLA3 #1/B VAL 410 N MLA35 #18/B HIS 407 O MLA3 #1/B VAL 410 H 3.070 2.126
MLA3 #1/B VAL 410 N MLA34 #19/B HIS 407 O MLA3 #1/B VAL 410 H 3.248 2.283
MLA3 #1/B VAL 410 N PWL2_cb1e6_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #21/B ASP 400 O MLA3 #1/B VAL 410 H 2.807 1.840
PWL2_HIPP43_12-11-2020-final.pdb #22/B ARG 44 NE (alt loc B) MLA3 #1/B VAL 410 O no hydrogen 2.805 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/C HOH 138 O MLA3 #1/B VAL 410 O no hydrogen 2.676 N/A
14 hydrogen bonds found
> hide #22.1 models
> show #22.1 models
> hide #22.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 22.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 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
> hide #23 models
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
> ui tool show H-Bonds
> hbonds sel radius 0.095 interModel false distSlop 0.5 angleSlop 22.0
> 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
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel radius 0.095 interModel false distSlop 0.8 angleSlop 22.0
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 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
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel radius 0.095 interModel false distSlop 0.8 angleSlop 30.0
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 30 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 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
> hide #!22 models
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 30.0 intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 30 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 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 30.0 twoColors true
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 30 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 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/B:410
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 30.0 twoColors true
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 30 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 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/B:410, #1/A:23
Expected an objects specifier or a keyword
> select #1/B:410 #1/A:23
40 atoms, 38 bonds, 1 pseudobond, 2 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.45 angleSlop 30.0
> twoColors true intraMol false intraRes false select true reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 30 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 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
0 strict hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.45 angleSlop 50.0
> twoColors true intraMol false intraRes false select true reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.45 angstroms and 50 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/B:410 #1/A:23
40 atoms, 38 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.6 angleSlop 30.0
> twoColors true intraMol false intraRes false select true reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.6 angstroms and 30 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 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
0 strict hydrogen bonds found
> show #1.1 models
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.45 angleSlop 22.0
> twoColors true intraMol false intraRes false select true reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.45 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/B:410 #1/A:23
40 atoms, 38 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.45 angleSlop 25.0
> twoColors true 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
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 23 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
0 strict hydrogen bonds found
> select #1/B:410 #1/A:23
40 atoms, 38 bonds, 1 pseudobond, 2 residues, 2 models selected
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel restrict both interModel false distSlop 0.45 angleSlop 25.0
> twoColors true slopColor #00bfff 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
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 23 NE MLA3 #1/B VAL 410 O MLA3 #1/A ARG 23 HE 2.851 2.304
1 hydrogen bonds found
0 strict hydrogen bonds found
> show #22.1 models
> hide #22.1 models
> hide #!22 models
> close #31
> close #21
> select add #1
8732 atoms, 8823 bonds, 1 pseudobond, 561 residues, 2 models selected
> hide #1.1 models
> select subtract #1.1
8732 atoms, 8823 bonds, 561 residues, 1 model selected
> show #1.1 models
> hide #1.1 models
> select add #1
8732 atoms, 8823 bonds, 1 pseudobond, 561 residues, 2 models selected
> select subtract #1.1
8732 atoms, 8823 bonds, 561 residues, 1 model selected
> view sel
Alignment identifier is 1/A
Alignment identifier is 1/B
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:397,405
37 atoms, 35 bonds, 2 residues, 1 model selected
> select #1/B:397,401,405
61 atoms, 58 bonds, 3 residues, 1 model selected
> select #1/B:397,401,405,410-411
98 atoms, 95 bonds, 5 residues, 1 model selected
> select #1/B:397,401,405,410-411,413
117 atoms, 113 bonds, 6 residues, 1 model selected
> select #1/B:397,401,405,410-411,413,415
136 atoms, 131 bonds, 7 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415
150 atoms, 145 bonds, 8 residues, 1 model selected
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:415-416
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #1/B:413,415-416
55 atoms, 53 bonds, 3 residues, 1 model selected
> select #1/B:410-411,413,415-416
92 atoms, 90 bonds, 5 residues, 1 model selected
> select #1/B:408,410-411,413,415-416
106 atoms, 104 bonds, 6 residues, 1 model selected
> select #1/B:405,408,410-411,413,415-416
128 atoms, 125 bonds, 7 residues, 1 model selected
> select #1/B:401,405,408,410-411,413,415-416
152 atoms, 148 bonds, 8 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415-416
167 atoms, 162 bonds, 9 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415-417
184 atoms, 179 bonds, 10 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415-417,420
208 atoms, 202 bonds, 11 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 25.0 twoColors true
> slopColor #00bfff 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 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 16 NH1 MLA3 #1/B GLU 397 OE2 MLA3 #1/A ARG 16 HH11 2.762 1.834
MLA3 #1/A ARG 16 NH2 MLA3 #1/B GLU 397 OE1 MLA3 #1/A ARG 16 HH22 2.805 1.967
MLA3 #1/A ARG 16 NH2 MLA3 #1/B GLU 397 OE2 MLA3 #1/A ARG 16 HH22 2.717 1.796
MLA3 #1/A SER 19 N MLA3 #1/B ILE 415 O MLA3 #1/A SER 19 H 2.893 1.910
MLA3 #1/A SER 19 OG MLA3 #1/B GLU 397 OE1 MLA3 #1/A SER 19 HG 2.597 1.697
MLA3 #1/A SER 21 N MLA3 #1/B ILE 413 O MLA3 #1/A SER 21 H 2.813 1.811
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
MLA3 #1/B ARG 401 NH1 MLA3 #1/A ASP 65 OD2 MLA3 #1/B ARG 401 HH12 2.726 1.717
MLA3 #1/B ARG 401 NH2 MLA3 #1/A ASP 65 OD2 MLA3 #1/B ARG 401 HH22 3.289 2.448
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
MLA3 #1/B ILE 413 N MLA3 #1/A SER 21 O MLA3 #1/B ILE 413 H 2.827 1.904
MLA3 #1/B ILE 415 N MLA3 #1/A SER 19 O MLA3 #1/B ILE 415 H 2.888 1.894
MLA3 #1/B GLN 416 NE2 MLA3 #1/A ASN 31 O MLA3 #1/B GLN 416 HE22 2.717 2.090
MLA3 #1/B MET 417 N MLA3 #1/A GLU 17 O MLA3 #1/B MET 417 H 2.777 1.769
MLA3 #1/B ARG 420 NH2 MLA3 #1/A GLU 15 OE1 MLA3 #1/B ARG 420 HH22 2.788 1.898
MLA3 #1/B ARG 420 NH2 MLA3 #1/A GLU 15 OE2 MLA3 #1/B ARG 420 HH22 2.858 2.132
22 hydrogen bonds found
15 strict hydrogen bonds found
> color sel byhetero
> show #1.1 models
> show sel atoms
[Repeated 1 time(s)]
> select #1/B:408
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:408
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/B:398
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/B:397-398
25 atoms, 24 bonds, 2 residues, 1 model selected
> select #1/B:397
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:397
15 atoms, 14 bonds, 1 residue, 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:397
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:397
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:397,401
39 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/B:397,401,405
61 atoms, 58 bonds, 3 residues, 1 model selected
> select #1/B:397,401,405,408
75 atoms, 72 bonds, 4 residues, 1 model selected
> select #1/B:397,401,405,408,410-411
112 atoms, 109 bonds, 6 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413
131 atoms, 127 bonds, 7 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415
150 atoms, 145 bonds, 8 residues, 1 model selected
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:416-417
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #1/B:415-417
53 atoms, 52 bonds, 3 residues, 1 model selected
> select #1/B:413,415-417
72 atoms, 70 bonds, 4 residues, 1 model selected
> select #1/B:410-411,413,415-417
109 atoms, 107 bonds, 6 residues, 1 model selected
> select #1/B:408,410-411,413,415-417
123 atoms, 121 bonds, 7 residues, 1 model selected
> select #1/B:405,408,410-411,413,415-417
145 atoms, 142 bonds, 8 residues, 1 model selected
> select #1/B:401,405,408,410-411,413,415-417
169 atoms, 165 bonds, 9 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415-417
184 atoms, 179 bonds, 10 residues, 1 model selected
> select #1/B:397,401,405,408,410-411,413,415-417,420
208 atoms, 202 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 25.0 twoColors true
> slopColor #00bfff 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 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 16 NH1 MLA3 #1/B GLU 397 OE2 MLA3 #1/A ARG 16 HH11 2.762 1.834
MLA3 #1/A ARG 16 NH2 MLA3 #1/B GLU 397 OE1 MLA3 #1/A ARG 16 HH22 2.805 1.967
MLA3 #1/A ARG 16 NH2 MLA3 #1/B GLU 397 OE2 MLA3 #1/A ARG 16 HH22 2.717 1.796
MLA3 #1/A SER 19 N MLA3 #1/B ILE 415 O MLA3 #1/A SER 19 H 2.893 1.910
MLA3 #1/A SER 19 OG MLA3 #1/B GLU 397 OE1 MLA3 #1/A SER 19 HG 2.597 1.697
MLA3 #1/A SER 21 N MLA3 #1/B ILE 413 O MLA3 #1/A SER 21 H 2.813 1.811
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
MLA3 #1/B ARG 401 NH1 MLA3 #1/A ASP 65 OD2 MLA3 #1/B ARG 401 HH12 2.726 1.717
MLA3 #1/B ARG 401 NH2 MLA3 #1/A ASP 65 OD2 MLA3 #1/B ARG 401 HH22 3.289 2.448
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
MLA3 #1/B ILE 413 N MLA3 #1/A SER 21 O MLA3 #1/B ILE 413 H 2.827 1.904
MLA3 #1/B ILE 415 N MLA3 #1/A SER 19 O MLA3 #1/B ILE 415 H 2.888 1.894
MLA3 #1/B GLN 416 NE2 MLA3 #1/A ASN 31 O MLA3 #1/B GLN 416 HE22 2.717 2.090
MLA3 #1/B MET 417 N MLA3 #1/A GLU 17 O MLA3 #1/B MET 417 H 2.777 1.769
MLA3 #1/B ARG 420 NH2 MLA3 #1/A GLU 15 OE1 MLA3 #1/B ARG 420 HH22 2.788 1.898
MLA3 #1/B ARG 420 NH2 MLA3 #1/A GLU 15 OE2 MLA3 #1/B ARG 420 HH22 2.858 2.132
22 hydrogen bonds found
15 strict hydrogen bonds found
> show sel atoms
> view sel
> select #1/A:21
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:21
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19,22
30 atoms, 28 bonds, 2 residues, 1 model selected
> select #1/A:21
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:21
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19,21
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/A:17
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:17
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/A:31
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:31
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:417
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:417
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:416
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/B:420
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:420
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:415
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:414-415
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #1/B:414
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:414
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:420
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:420
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405-406
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select #1/A:41
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:41
12 atoms, 11 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
[Repeated 1 time(s)]
> show sel atoms
> show #!22 models
> select add #22
1652 atoms, 1517 bonds, 1 pseudobond, 363 residues, 3 models selected
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 22/A
Alignment identifier is 22/B
> select #22/B:62
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:62
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 25.0 twoColors true
> slopColor #00bfff 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:
22 PWL2_HIPP43_12-11-2020-final.pdb
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PWL2_HIPP43_12-11-2020-final.pdb #22/A ASN 32 ND2 PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 OD2 no hydrogen 2.873 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A ARG 67 NE PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 OD2 no hydrogen 2.736 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/A VAL 96 N PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 O no hydrogen 2.827 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 N PWL2_HIPP43_12-11-2020-final.pdb #22/A PRO 94 O no hydrogen 2.975 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/C HOH 36 O PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 OD1 no hydrogen 2.487 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/C HOH 43 O PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 OD1 no hydrogen 2.909 N/A
PWL2_HIPP43_12-11-2020-final.pdb #22/C HOH 43 O PWL2_HIPP43_12-11-2020-final.pdb #22/B ASP 62 OD2 no hydrogen 3.607 N/A
7 hydrogen bonds found
6 strict hydrogen bonds found
> ui tool show H-Bonds
> show sel atoms
> show #23 models
> hide #23 models
> show #22.1 models
> hide #!1 models
> select #22/A:43
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:43
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1.1
9 atoms, 8 bonds, 22 pseudobonds, 1 residue, 2 models selected
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> show #!1 models
> select #1/B:420
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:420
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:414
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:414
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!22 models
> hide #22.1 models
> view sel
> show sel atoms
> style sel stick
Changed 11 atom styles
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 25.0 twoColors true
> slopColor #00bfff 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
> view
> select subtract #1.1
Nothing selected
> select #1/A:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #1.1 models
> show #1.1 models
> view sel
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 25.0 twoColors true
> slopColor #00bfff 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
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A SER 19 N MLA3 #1/B ILE 415 O MLA3 #1/A SER 19 H 2.893 1.910
MLA3 #1/A SER 19 OG MLA3 #1/B GLU 397 OE1 MLA3 #1/A SER 19 HG 2.597 1.697
MLA3 #1/B ILE 415 N MLA3 #1/A SER 19 O MLA3 #1/B ILE 415 H 2.888 1.894
3 hydrogen bonds found
3 strict hydrogen bonds found
> select #1/B:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> view sel
> show sel atoms
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel interModel false distSlop 0.45 angleSlop 25.0 twoColors true
> slopColor #00bfff 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 16 N MLA3 #1/B ILE 421 O MLA3 #1/A ARG 16 H 3.146 2.215
MLA3 #1/B ILE 421 N MLA3 #1/A ARG 16 O MLA3 #1/B ILE 421 H 2.932 1.966
2 hydrogen bonds found
2 strict hydrogen bonds found
> select #1/B:414
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:414
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/B:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:16
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/A:16
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel dashes 8 interModel false distSlop 0.45 angleSlop 25.0 twoColors
> true slopColor #00bfff 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
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
MLA3 #1/A ARG 16 N MLA3 #1/B ILE 421 O MLA3 #1/A ARG 16 H 3.146 2.215
MLA3 #1/A ARG 16 NH1 MLA3 #1/B GLU 397 OE2 MLA3 #1/A ARG 16 HH11 2.762 1.834
MLA3 #1/A ARG 16 NH2 MLA3 #1/B GLU 397 OE1 MLA3 #1/A ARG 16 HH22 2.805 1.967
MLA3 #1/A ARG 16 NH2 MLA3 #1/B GLU 397 OE2 MLA3 #1/A ARG 16 HH22 2.717 1.796
MLA3 #1/B ILE 421 N MLA3 #1/A ARG 16 O MLA3 #1/B ILE 421 H 2.932 1.966
5 hydrogen bonds found
4 strict hydrogen bonds found
> show #!22 models
> select #1/B:371-421
824 atoms, 831 bonds, 51 residues, 1 model selected
> select #1/B:371-421
824 atoms, 831 bonds, 51 residues, 1 model selected
> select #1/B:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:421
19 atoms, 18 bonds, 1 residue, 1 model selected
> show #22.1 models
> hide #!22 models
> hide #22.1 models
> hide #1.1 models
> select add #1
8732 atoms, 8823 bonds, 5 pseudobonds, 561 residues, 2 models selected
> hide sel atoms
> select #1/B:356-406
754 atoms, 757 bonds, 51 residues, 1 model selected
> select #1/B:356-406
754 atoms, 757 bonds, 51 residues, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> hbonds sel reveal true
25 hydrogen bonds found
> show #23 models
> ui tool show H-Bonds
> select #1/A:68
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:68
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:68,72
27 atoms, 25 bonds, 2 residues, 1 model selected
> select #1/A:65,68,72
39 atoms, 36 bonds, 3 residues, 1 model selected
> select #1/A:6
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:6
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:6,68
29 atoms, 27 bonds, 2 residues, 1 model selected
> select #1/A:6,68,72
41 atoms, 38 bonds, 3 residues, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:6
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:6
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide #23 models
> select #1/A:405, #1/B:6,68,72
Expected an objects specifier or a keyword
> select #1/A:405 #1/B:6,68,72
42 atoms, 39 bonds, 3 residues, 1 model selected
> select #1/A:405 #1/B:6,68,72
42 atoms, 39 bonds, 3 residues, 1 model selected
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 4 pseudobonds, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel dashes 8 restrict both interModel false distSlop 0.45 angleSlop
> 25.0 twoColors true slopColor #00bfff 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
> color bfactor sel
7 atoms, 4 residues, atom bfactor range 87.1 to 96.9
> undo
> view sel
> 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) #00bffffe
> color (#!1 & sel) #00bfffc4
> color (#!1 & sel) #00bfffaf
> color (#!1 & sel) #00bfff87
> color (#!1 & sel) #00bfff7f
> color (#!1 & sel) #00bfff70
> color (#!1 & sel) #00bfff6e
> color (#!1 & sel) #00bfff69
> color (#!1 & sel) #00bfff67
> color (#!1 & sel) #00bfff58
> color (#!1 & sel) #00bfff50
> color (#!1 & sel) #00bfff4e
> color (#!1 & sel) #00bfff44
> color (#!1 & sel) #9bffef44
> color (#!1 & sel) #5de0ff44
> color (#!1 & sel) #5de0ff42
> show sel cartoons
> transparency (#!1 & sel) 40
> show sel cartoons
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> view sel
> show sel cartoons
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting shadows true
> lighting shadows false
> color (#!1 & sel) #5de0ff44
> color (#!1 & sel) #5de0ffd2
> color (#!1 & sel) #5de0ffeb
> color (#!1 & sel) #5de0ffff
> color (#!1 & sel) #9dfcffff
> color (#!1 & sel) #81ffe8ff
> color (#!1 & sel) #50ffe6ff
> color (#!1 & sel) #72fff4ff
> 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 cartoons
[Repeated 2 time(s)]
> hide sel cartoons
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> color (#!1 & sel) #72fff4fc
> color (#!1 & sel) #72fff4a8
> color (#!1 & sel) #72fff48c
> color (#!1 & sel) #72fff47a
> color (#!1 & sel) #72fff464
> color (#!1 & sel) #72fff45b
> color (#!1 & sel) #72fff454
> color (#!1 & sel) #72fff451
> color (#!1 & sel) #72fff452
> color (#!1 & sel) #72fff49e
> color (#!1 & sel) #72fff4c5
> color (#!1 & sel) #72fff4f3
> color (#!1 & sel) #72fff4ff
> undo
[Repeated 9 time(s)]
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting soft
> color sel #f7c0f9ff
> 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
> select add #1.2
1832 atoms, 1864 bonds, 124 residues, 4 models selected
> select subtract #1.2
1 model selected
> select add #1.2
1832 atoms, 124 residues, 3 models selected
> show sel surfaces
> show sel cartoons
> select #1/A:102
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:102-124
360 atoms, 366 bonds, 23 residues, 1 model selected
> select #1/A:92-93
31 atoms, 31 bonds, 2 residues, 1 model selected
> select #1/A:92-124
479 atoms, 488 bonds, 33 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 cartoons
> color (#!1 & sel) #9ef5f6ff
> color (#!1 & sel) #84f6d2ff
[Repeated 1 time(s)]
> color (#!1 & sel) #84f6d2c4
> color (#!1 & sel) #84f6d230
> color (#!1 & sel) #84f6d200
> color (#!1 & sel) #84f6d20b
> color (#!1 & sel) #84f6d22f
> color (#!1 & sel) #84f6d24f
> color (#!1 & sel) #84f6d25f
> color (#!1 & sel) #84f6d274
> color (#!1 & sel) #84f6d293
> color (#!1 & sel) #84f6d29e
> color (#!1 & sel) #84f6d29f
> color (#!1 & sel) #84f6d2a0
> color (#!1 & sel) #84f6d2a6
> color (#!1 & sel) #84f6d2b5
> color (#!1 & sel) #84f6d2d8
> color (#!1 & sel) #84f6d2e6
> color (#!1 & sel) #84f6d2f5
> color (#!1 & sel) #84f6d2ff
> color (#!1 & sel) #84f6d2f6
> color (#!1 & sel) #84f6d2e6
> color (#!1 & sel) #84f6d2db
> color (#!1 & sel) #84f6d2ce
> color (#!1 & sel) #84f6d2c7
[Repeated 1 time(s)]
> color (#!1 & sel) #84f6d2c8
> color (#!1 & sel) #84f6d2d0
> color (#!1 & sel) #84f6d2d3
> color (#!1 & sel) #84f6d2d5
> color (#!1 & sel) #84f6d2dc
> color (#!1 & sel) #84f6d2dd
> color (#!1 & sel) #84f6d2ef
> color (#!1 & sel) #84f6d2fa
> color (#!1 & sel) #84f6d2f9
> color (#!1 & sel) #84f6d2f4
> color (#!1 & sel) #84f6d2e9
> color (#!1 & sel) #84f6d2d5
> color (#!1 & sel) #84f6d2d4
> color (#!1 & sel) #84f6d2fb
> color (#!1 & sel) #84f6d2ff
> color (#!1 & sel) #84f6d2f2
> color (#!1 & sel) #84f6d2d7
> color (#!1 & sel) #84f6d2d4
> color (#!1 & sel) #84f6d2c2
> color (#!1 & sel) #84f6d2a7
> color (#!1 & sel) #84f6d2a6
> color (#!1 & sel) #84f6d2a7
> color (#!1 & sel) #84f6d2b9
> color (#!1 & sel) #84f6d2d4
> color (#!1 & sel) #84f6d2ec
> color (#!1 & sel) #84f6d2f6
> color (#!1 & sel) #84f6d2fd
> color (#!1 & sel) #84f6d2ff
> color (#!1 & sel) #84f6d2f5
> color (#!1 & sel) #84f6d2ec
> color (#!1 & sel) #84f6d2ea
> color (#!1 & sel) #84f6d2d8
> color (#!1 & sel) #84f6d2ce
> color (#!1 & sel) #84f6d2cc
> color (#!1 & sel) #84f6d2c8
> color (#!1 & sel) #84f6d2bc
> color (#!1 & sel) #84f6d2b6
> color (#!1 & sel) #84f6d2b8
> color (#!1 & sel) #84f6d2e0
> color (#!1 & sel) #84f6d2ff
> color (#!1 & sel) #a7f6ddff
> color (#!1 & sel) #97e4f6ff
> color (#!1 & sel) #79ebf6ff
> color (#!1 & sel) #5ff6f5ff
> color (#!1 & sel) #67e6f6ff
> color (#!1 & sel) #81eff6ff
> color (#!1 & sel) #65f6edff
> hide sel surfaces
> color (#!1 & sel) #65f6edf8
> color (#!1 & sel) #65f6edbf
> color (#!1 & sel) #65f6edac
> color (#!1 & sel) #65f6eda8
> color (#!1 & sel) #65f6ed9c
[Repeated 1 time(s)]
> color (#!1 & sel) #65f6eda5
> color (#!1 & sel) #65f6edda
> color (#!1 & sel) #65f6edff
> transparency (#!1 & sel) 80
> show sel surfaces
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 80
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> view sel
> color sel byhetero
> undo
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> color sel byhetero
> undo
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> select add #1.2
1832 atoms, 1864 bonds, 124 residues, 4 models selected
> select subtract #1.2
1 model selected
> select add #1.2
1832 atoms, 124 residues, 3 models selected
> select subtract #1.2
1 model selected
> select add #1.2
1832 atoms, 124 residues, 3 models selected
> select subtract #1.2
1 model selected
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> select add #1.2
1854 atoms, 59 bonds, 8 pseudobonds, 125 residues, 6 models selected
> select subtract #1.2
22 atoms, 21 bonds, 1 residue, 2 models selected
> select add #1
8732 atoms, 8823 bonds, 9 pseudobonds, 561 residues, 5 models selected
> select subtract #1
1 model selected
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> hide sel surfaces
> color sel byhetero
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> select add #1.2
1854 atoms, 59 bonds, 8 pseudobonds, 125 residues, 7 models selected
> select subtract #1.2
22 atoms, 21 bonds, 1 residue, 3 models selected
> rotate x 120
Unknown command: rotate x 120
> turn x 120 models #1
> view sel
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting flat
> graphics silhouettes false
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> view sel
> select subtract #1.3
1 model selected
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 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
> select subtract #1.3
4 atoms, 3 residues, 3 models selected
> select add #1.2
1832 atoms, 124 residues, 4 models selected
> select subtract #1.2
1 model selected
> select #1/B:1
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B
6900 atoms, 6959 bonds, 1 pseudobond, 437 residues, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 90
> hide #!1 models
> show #!1 models
> select add #1
8732 atoms, 8823 bonds, 9 pseudobonds, 561 residues, 6 models selected
> select subtract #1
2 models selected
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #!1.3 models
> show #1.3 models
> hide #1.2 models
> show #1.2 models
> select #1/B:1-2
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B
6900 atoms, 6959 bonds, 1 pseudobond, 437 residues, 2 models selected
> transparency (#!1 & sel) 80
> select #1/A
1832 atoms, 1864 bonds, 124 residues, 1 model selected
> select #1/A:57-58
28 atoms, 29 bonds, 2 residues, 1 model selected
> select #1/A:57-124
996 atoms, 1017 bonds, 68 residues, 1 model selected
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:1-54
812 atoms, 822 bonds, 54 residues, 1 model selected
> select #1/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:1-4
47 atoms, 48 bonds, 4 residues, 1 model selected
> select #1/A:4-10,16-23,27-31,43-49,52-54,61-64
557 atoms, 558 bonds, 34 residues, 1 model selected
> select #1/A:11
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:11-24
222 atoms, 221 bonds, 14 residues, 1 model selected
> select #1/A:8-9
37 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/A:8-10
58 atoms, 59 bonds, 3 residues, 1 model selected
> select #1/A:8
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:8-17
167 atoms, 168 bonds, 10 residues, 1 model selected
> hide #1/A:8-17
> hide cartoons #1/A:8-17
Expected ',' or a keyword
> hide sel cartoons
> select #1/A:18-19
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/A:18-23
91 atoms, 90 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #1/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:61-64
51 atoms, 51 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1/A:84
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:84-124
572 atoms, 583 bonds, 41 residues, 1 model selected
> hide sel cartoons
> select #1/A:80-81
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #1/A:80-83
61 atoms, 62 bonds, 4 residues, 1 model selected
> select #1/A:24
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:24-26
40 atoms, 39 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405-406
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for MLA3_B SES surface #1.3: minimum, -13.05, mean -0.10,
maximum 14.18
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1/B:1
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B
6900 atoms, 6959 bonds, 1 pseudobond, 437 residues, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 90
> transparency (#!1 & sel) 80
> select #1/B:425-426
27 atoms, 27 bonds, 2 residues, 1 model selected
> select #1/B:425-437
193 atoms, 196 bonds, 13 residues, 1 model selected
> select #1/B:419-420
38 atoms, 38 bonds, 2 residues, 1 model selected
> select #1/B:419-424
96 atoms, 96 bonds, 6 residues, 1 model selected
> select #1/B:437
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:419-437
289 atoms, 293 bonds, 19 residues, 1 model selected
> hide sel surfaces
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> 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
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
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
> select #1/B:1
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B
6900 atoms, 6959 bonds, 1 pseudobond, 437 residues, 2 models selected
> hide sel surfaces
> view sel
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405-406
32 atoms, 31 bonds, 2 residues, 1 model selected
> view sel
> ~display HC
> ~display C
> ~display CH
> hide CH
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display CH
> hide CH
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display CH
> hide CH
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display CH
> hide CH
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> ~display HC
> select add #1.3
6941 atoms, 59 bonds, 8 pseudobonds, 440 residues, 7 models selected
> select subtract #1.3
41 atoms, 38 bonds, 3 residues, 3 models selected
> select add #1.2
1832 atoms, 38 bonds, 124 residues, 4 models selected
> select subtract #1.2
1 model selected
> lighting soft
> lighting full
> lighting shadows false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> select #1/B:405 a #1/A:6,68,72 a
Expected a keyword
> select #1/B:405a #1/A:6,68,72 a
Expected a keyword
> select #1/B:405 #1/A:6,68,72
63 atoms, 59 bonds, 8 pseudobonds, 4 residues, 3 models selected
> color #1.1 #f38ed5ff models
> select add #1
8732 atoms, 8823 bonds, 9 pseudobonds, 561 residues, 9 models selected
> select subtract #1
2 models selected
> select add #1.1
4 pseudobonds, 1 model selected
> color #1.1 #f39959ff models
> color #1.1 #7ff3b1ff models
> color #1.1 #71f3d8ff models
> color #1.1 #83d0f3ff models
> color #1.1 #466ef3ff models
> color #1.1 #8cb1f3ff models
> select subtract #1.1
Nothing selected
> color #1.1 #277ef3ff models
> color #1.1 #3fdaf3ff models
> color #1.1 #95f3edff models
> color #1.1 #ed96f3ff models
> color #1.1 #dc51f3ff models
> color #1.1 #e9f381ff models
> color #1.1 #d1f350ff models
> color #1.1 #cbf37cff models
> color #1.1 #f3e03fff models
> color #1.1 #ffec42ff models
> color #1.1 #fff199ff models
> color #1.1 #fff254ff models
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:405
22 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> center #1/B:405
Unknown command: center #1/B:405
> center #1/B:405
Unknown command: center #1/B:405
> centre #1/B:405
Unknown command: centre #1/B:405
> center
Unknown command: center
> center
Unknown command: center
> centre
Unknown command: centre
> view #1/B:405
> 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 cartoons
> select add #1.2
1832 atoms, 1864 bonds, 124 residues, 4 models selected
> select subtract #1.2
1 model selected
> view orient
> view #1/B:405
> graphics silhouettes true
> show #22 models
> 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/A:84
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:84
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:51-52
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #22/A:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/B:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:23
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B
883 atoms, 915 bonds, 112 residues, 1 model selected
> color sel cyan
> ui tool show "Color Actions"
> color sel #6bfffaff
> color sel #8effecff
> select #22/A:26-27
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #22/A
582 atoms, 591 bonds, 75 residues, 1 model selected
> color sel #97ffbbff
> color sel #74ffa2ff
> color sel #56ff6aff
> color sel #48ff82ff
> color sel #36bf61ff
> color sel #3cd46cff
> color sel #69d487ff
> color sel #39d46cff
> color sel #b5d484ff
> color sel #9cd49cff
> color sel #8bd46cff
> color sel #8bd56cff
> color sel #9df17aff
> color sel #a7ff81ff
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> select #22/B:93,89,27 #22/A:51
34 atoms, 30 bonds, 4 residues, 1 model selected
> color sel byhetero
> hbonds sel reveal true
37 hydrogen bonds found
> show #23 models
> hide #23 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:
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 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
4 hydrogen bonds found
1 strict hydrogen bonds found
> hide #!1 models
> undo
[Repeated 4 time(s)]
> select #22/B:93,89,27 #22/A:51
34 atoms, 30 bonds, 10 pseudobonds, 4 residues, 3 models selected
> ~display HC
> ~display C
> select #22/B:93,89,27 #22/A:51
34 atoms, 30 bonds, 10 pseudobonds, 4 residues, 3 models selected
> hide #!1 models
> color sel byhetero
> ui tool show H-Bonds
> ui tool show "Check Waters"
> hbonds #22/C interModel false reveal true restrict any name "water H-bonds"
477 hydrogen bonds found
> select #22/C
175 atoms, 206 pseudobonds, 175 residues, 2 models selected
> display #22/C :<4
> view #22/C @<4
No waters chosen
> select #22/C:54
1 atom, 1 residue, 1 model selected
> display #22/C:54 :<4
> view #22/C:54 @<4
> select #22/C:54,112
2 atoms, 2 residues, 1 model selected
> display #22/C:54,112 :<4
> view #22/C:54,112 @<4
> select #22/C:54,112,135
3 atoms, 3 residues, 1 model selected
> display #22/C:54,112,135 :<4
> view #22/C:54,112,135 @<4
> select #22/C:54,112,135,150
4 atoms, 4 residues, 1 model selected
> display #22/C:54,112,135,150 :<4
> view #22/C:54,112,135,150 @<4
> select #22/C:54,112,135,150,196
5 atoms, 5 residues, 1 model selected
> display #22/C:54,112,135,150,196 :<4
> view #22/C:54,112,135,150,196 @<4
> select #22/C:54,107,112,135,150,196
6 atoms, 6 residues, 1 model selected
> display #22/C:54,107,112,135,150,196 :<4
> view #22/C:54,107,112,135,150,196 @<4
> select #22/C:54,107-108,112,135,150,196
7 atoms, 7 residues, 1 model selected
> display #22/C:54,107-108,112,135,150,196 :<4
> view #22/C:54,107-108,112,135,150,196 @<4
> select #22/C:54,107-108,112,128,135,150,196
8 atoms, 8 residues, 1 model selected
> display #22/C:54,107-108,112,128,135,150,196 :<4
> view #22/C:54,107-108,112,128,135,150,196 @<4
> select #22/C:54,107-108,112,128,135,143,150,196
9 atoms, 9 residues, 1 model selected
> display #22/C:54,107-108,112,128,135,143,150,196 :<4
> view #22/C:54,107-108,112,128,135,143,150,196 @<4
> select #22/C:54,107-108,112,128,135,143,150-151,196
10 atoms, 10 residues, 1 model selected
> display #22/C:54,107-108,112,128,135,143,150-151,196 :<4
> view #22/C:54,107-108,112,128,135,143,150-151,196 @<4
> select #22/C:54,107-108,112,128,135,143,150-152,196
11 atoms, 11 residues, 1 model selected
> display #22/C:54,107-108,112,128,135,143,150-152,196 :<4
> view #22/C:54,107-108,112,128,135,143,150-152,196 @<4
> select #22/C:16,54,107-108,112,128,135,143,150-152,196
12 atoms, 12 residues, 1 model selected
> display #22/C:16,54,107-108,112,128,135,143,150-152,196 :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,196 @<4
> select #22/C:16,54,107-108,112,128,135,143,150-152,160,196
13 atoms, 13 residues, 1 model selected
> display #22/C:16,54,107-108,112,128,135,143,150-152,160,196 :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,160,196 @<4
> select #22/C:16,54,107-108,112,128,135,143,150-152,160,169,196
14 atoms, 14 residues, 1 model selected
> display #22/C:16,54,107-108,112,128,135,143,150-152,160,169,196 :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,160,169,196 @<4
> select #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,196
15 atoms, 15 residues, 1 model selected
> display #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,196 :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,196 @<4
> select #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,189,196
16 atoms, 16 residues, 1 model selected
> display #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,189,196 :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,189,196 @<4
> select #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,187,189,196
17 atoms, 17 residues, 1 model selected
> display #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,187,189,196
> :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,187,189,196 @<4
> select
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,181,187,189,196
18 atoms, 18 residues, 1 model selected
> display
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,181,187,189,196 :<4
> view #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,181,187,189,196
> @<4
> select
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,177,181,187,189,196
19 atoms, 19 residues, 1 model selected
> display
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,177,181,187,189,196
> :<4
> view
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,177,181,187,189,196
> @<4
> select
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,175,177,181,187,189,196
20 atoms, 20 residues, 1 model selected
> display
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,175,177,181,187,189,196
> :<4
> view
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,175,177,181,187,189,196
> @<4
> select
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
21 atoms, 21 residues, 1 model selected
> display
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
> :<4
> view
> #22/C:16,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
> @<4
> select
> #22/C:16,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
22 atoms, 22 residues, 1 model selected
> display
> #22/C:16,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
> :<4
> view
> #22/C:16,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
> @<4
> select
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
23 atoms, 23 residues, 1 model selected
> display
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
> :<4
> view
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,196
> @<4
> select
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,195-196
24 atoms, 24 residues, 1 model selected
> display
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,195-196
> :<4
> view
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,195-196
> @<4
> select
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,195-196
25 atoms, 25 residues, 1 model selected
> display
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,195-196
> :<4
> view
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,195-196
> @<4
> select
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
26 atoms, 26 residues, 1 model selected
> display
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
27 atoms, 27 residues, 1 model selected
> display
> #22/C:16,29,48,54,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
28 atoms, 28 residues, 1 model selected
> display
> #22/C:16,29,48,54,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
27 atoms, 27 residues, 1 model selected
> display
> #22/C:16,29,48,54,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
28 atoms, 28 residues, 1 model selected
> display
> #22/C:16,29,48,54,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,73,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
29 atoms, 29 residues, 1 model selected
> display
> #22/C:16,29,48,54,73,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,73,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
30 atoms, 30 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
31 atoms, 31 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
32 atoms, 32 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,91,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
33 atoms, 33 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,91,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,91,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
34 atoms, 34 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,107-108,112,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,107-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
35 atoms, 35 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,107-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,107-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,106-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
36 atoms, 36 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,106-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,106-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
37 atoms, 37 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,99,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
38 atoms, 38 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,99,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,99,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
39 atoms, 39 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
40 atoms, 40 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,137-138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
41 atoms, 41 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,137-138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128,135,137-138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
42 atoms, 42 residues, 1 model selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-152,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
43 atoms, 4 pseudobonds, 43 residues, 2 models selected
> display
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
44 atoms, 4 pseudobonds, 44 residues, 2 models selected
> display
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,147,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
45 atoms, 6 pseudobonds, 45 residues, 2 models selected
> display
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,147,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,143,147,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
46 atoms, 6 pseudobonds, 46 residues, 2 models selected
> display
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169,171,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169,171-172,175,177,181,187,189,191,193,195-196
47 atoms, 8 pseudobonds, 47 residues, 2 models selected
> display
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169,171-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169,171-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169-172,175,177,181,187,189,191,193,195-196
48 atoms, 8 pseudobonds, 48 residues, 2 models selected
> display
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-16,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169-172,175,177,181,187,189,191,193,195-196
49 atoms, 8 pseudobonds, 49 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167,169-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167-172,175,177,181,187,189,191,193,195-196
50 atoms, 8 pseudobonds, 50 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,167-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,166-172,175,177,181,187,189,191,193,195-196
51 atoms, 10 pseudobonds, 51 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,166-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,160,166-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,159-160,166-172,175,177,181,187,189,191,193,195-196
52 atoms, 10 pseudobonds, 52 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,159-160,166-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-153,159-160,166-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-154,159-160,166-172,175,177,181,187,189,191,193,195-196
53 atoms, 10 pseudobonds, 53 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-154,159-160,166-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-154,159-160,166-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,181,187,189,191,193,195-196
54 atoms, 10 pseudobonds, 54 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,181,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,181,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,181-182,187,189,191,193,195-196
55 atoms, 10 pseudobonds, 55 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,181-182,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,181-182,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,180-182,187,189,191,193,195-196
56 atoms, 10 pseudobonds, 56 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,180-182,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,180-182,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,179-182,187,189,191,193,195-196
57 atoms, 10 pseudobonds, 57 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,179-182,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,175,177,179-182,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189,191,193,195-196
58 atoms, 10 pseudobonds, 58 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189,191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189,191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196
59 atoms, 10 pseudobonds, 59 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,203
60 atoms, 10 pseudobonds, 60 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,203
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,203
> @<4
> select
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,202-203
61 atoms, 12 pseudobonds, 61 residues, 2 models selected
> display
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,202-203
> :<4
> view
> #22/C:15-17,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,202-203
> @<4
> select
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,202-203
62 atoms, 12 pseudobonds, 62 residues, 2 models selected
> display
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,202-203
> :<4
> view
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-196,202-203
> @<4
> select
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-197,202-203
63 atoms, 12 pseudobonds, 63 residues, 2 models selected
> display
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-197,202-203
> :<4
> view
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193,195-197,202-203
> @<4
> select
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
64 atoms, 14 pseudobonds, 64 residues, 2 models selected
> display
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20,29,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20,29,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
65 atoms, 14 pseudobonds, 65 residues, 2 models selected
> display
> #22/C:15-17,20,29,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20,29,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20,29,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
66 atoms, 14 pseudobonds, 66 residues, 2 models selected
> display
> #22/C:15-17,20,29,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20,29,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20,29-30,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
67 atoms, 14 pseudobonds, 67 residues, 2 models selected
> display
> #22/C:15-17,20,29-30,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20,29-30,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
68 atoms, 14 pseudobonds, 68 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
69 atoms, 14 pseudobonds, 69 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
70 atoms, 14 pseudobonds, 70 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
71 atoms, 16 pseudobonds, 71 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
72 atoms, 16 pseudobonds, 72 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
73 atoms, 16 pseudobonds, 73 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
74 atoms, 18 pseudobonds, 74 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
75 atoms, 18 pseudobonds, 75 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
76 atoms, 18 pseudobonds, 76 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-73,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-74,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
77 atoms, 18 pseudobonds, 77 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-74,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-74,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-75,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
78 atoms, 20 pseudobonds, 78 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-75,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-75,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-76,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
79 atoms, 20 pseudobonds, 79 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-76,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-76,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
80 atoms, 20 pseudobonds, 80 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
81 atoms, 22 pseudobonds, 81 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-82,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
82 atoms, 22 pseudobonds, 82 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-91,93-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
83 atoms, 22 pseudobonds, 83 residues, 2 models selected
> display
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
84 atoms, 22 pseudobonds, 84 residues, 2 models selected
> display
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97,99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
85 atoms, 22 pseudobonds, 85 residues, 2 models selected
> display
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-99,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
86 atoms, 22 pseudobonds, 86 residues, 2 models selected
> display
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,116-117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
87 atoms, 24 pseudobonds, 87 residues, 2 models selected
> display
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,116-117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,116-117,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
88 atoms, 26 pseudobonds, 88 residues, 2 models selected
> display
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-108,112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
89 atoms, 26 pseudobonds, 89 residues, 2 models selected
> display
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
90 atoms, 26 pseudobonds, 90 residues, 2 models selected
> display
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-100,105-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
91 atoms, 26 pseudobonds, 91 residues, 2 models selected
> display
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,142-143,147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,142-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
92 atoms, 26 pseudobonds, 92 residues, 2 models selected
> display
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,142-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,142-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
93 atoms, 26 pseudobonds, 93 residues, 2 models selected
> display
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,15-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,14-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
94 atoms, 28 pseudobonds, 94 residues, 2 models selected
> display
> #22/C:10-11,14-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,14-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-135,137-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,14-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
95 atoms, 28 pseudobonds, 95 residues, 2 models selected
> display
> #22/C:10-11,14-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,14-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
96 atoms, 30 pseudobonds, 96 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-147,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-148,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
97 atoms, 34 pseudobonds, 97 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-148,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-148,150-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
98 atoms, 34 pseudobonds, 98 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-155,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
99 atoms, 34 pseudobonds, 99 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,159-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
100 atoms, 34 pseudobonds, 100 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,163,166-172,174-175,177,179-182,187,189-191,193-197,202-203
101 atoms, 36 pseudobonds, 101 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,163,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,54,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,163,166-172,174-175,177,179-182,187,189-191,193-197,202-203
> @<4
> select #22/C:178
1 atom, 1 residue, 1 model selected
> display #22/C:178 :<4
> view #22/C:178 @<4
> select
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,163-164,166-175,177-182,187,189-191,193-197,202-203
103 atoms, 36 pseudobonds, 103 residues, 2 models selected
> display
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,163-164,166-175,177-182,187,189-191,193-197,202-203
> :<4
> view
> #22/C:10-11,13-17,20-21,29-30,32,34-35,37,46,48,57,60-62,66-67,72-77,81-84,88,90-94,97-112,116-117,126,128-138,141-156,158-160,163-164,166-175,177-182,187,189-191,193-197,202-203
> @<4
> select
> #22/C:1-9,12,18-19,22-28,31,33,36,38-45,47,49-56,58-59,63-65,68-71,79,85-86,89,95,115,120-124,127,139-140,157,161-162,165,176,178,183-186,188,192,198-199
73 atoms, 58 pseudobonds, 73 residues, 2 models selected
> display
> #22/C:1-9,12,18-19,22-28,31,33,36,38-45,47,49-56,58-59,63-65,68-71,79,85-86,89,95,115,120-124,127,139-140,157,161-162,165,176,178,183-186,188,192,198-199
> :<4
> view
> #22/C:1-9,12,18-19,22-28,31,33,36,38-45,47,49-56,58-59,63-65,68-71,79,85-86,89,95,115,120-124,127,139-140,157,161-162,165,176,178,183-186,188,192,198-199
> @<4
> 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
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