ChimeraX Log

coulombic

Coulombic values for AF-A1Z1D6-F1-model_v4.cif_A SES surface #1.1: minimum, -13.99, mean -2.80, maximum 7.54
To also show corresponding color key, enter the above coulombic command and add key true

hide #1.1 models

open 6yez

6yez title:
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]

Chain information for 6yez #2
Chain	Description	UniProt
1	Lhca1
2	Chlorophyll a-b binding protein, chloroplastic	Q41038_PEA
3	Chlorophyll a-b binding protein 3, chloroplastic	CB23_PEA
4	Chlorophyll a-b binding protein P4, chloroplastic	CB24_PEA
A	Photosystem I P700 chlorophyll a apoprotein A1	A0A0F6NFW5_PEA
B	Photosystem I P700 chlorophyll a apoprotein A2	A0A0F6NGI2_PEA
C	Photosystem I iron-sulfur center	PSAC_PEA
D	PsaD
E	PsaE
F	PsaF
G	PsaG
H	PsaH
I	Photosystem I reaction center subunit VIII	PSAI_PEA
J	PsaJ
K	Photosystem I reaction center subunit X psaK	E1C9L3_PEA
L	PsaL
N	Ferredoxin-1, chloroplastic	FER1_PEA
P	Plastocyanin

Non-standard residues in 6yez #2
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
C7Z — (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol ((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)

select #2

39226 atoms, 40742 bonds, 678 pseudobonds, 3684 residues, 2 models selected

hide sel atoms

select #2/A-E/N

21037 atoms, 21881 bonds, 372 pseudobonds, 1981 residues, 2 models selected

show sel cartoons

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

select #2/N &protein

724 atoms, 736 bonds, 97 residues, 1 model selected

coulombic sel

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_N SES surface #2.2: minimum, -22.35, mean -7.76, maximum 6.07
To also show corresponding color key, enter the above coulombic command and add key true

ui mousemode right "translate selected models"

select #1

369 atoms, 372 bonds, 54 residues, 1 model selected

view matrix models #1,1,0,0,38.794,0,1,0,146.26,0,0,1,93.086

view matrix models #1,1,0,0,80.971,0,1,0,155.21,0,0,1,92.043

view matrix models #1,1,0,0,118.66,0,1,0,188.05,0,0,1,73.54

save "/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs"

show #1.1 models

hide #1.1 models

hide #2.2 models

select #2/N:Cys

30 atoms, 25 bonds, 5 residues, 1 model selected

show sel atoms

style sel stick

Changed 30 atom styles

color sel byhetero

select #2/N:18

6 atoms, 5 bonds, 1 residue, 1 model selected

hide sel atoms

select #2/N:39,44,47,77

24 atoms, 20 bonds, 4 residues, 1 model selected

select #1

369 atoms, 372 bonds, 54 residues, 1 model selected

view matrix models #1,1,0,0,125.11,0,1,0,180.57,0,0,1,83.231

view matrix models #1,1,0,0,124.62,0,1,0,176.17,0,0,1,84.747

show #1.1 models

ui mousemode right "rotate selected models"

view matrix models #1,0.45679,-0.5223,-0.7201,126.73,0.84237,0.51416,0.16142,175.23,0.28594,-0.68032,0.67483,85.358

transparency (#!1 & sel) 50

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

show #2.2 models

transparency (#!2 & sel) 50

select #1

369 atoms, 372 bonds, 54 residues, 1 model selected

hide #1.1 models

hide #2.2 models

ui mousemode right "move picked models"

view matrix models #2,1,0,0,-0.12823,0,1,0,-1.3842,0,0,1,0.015386

select #1

369 atoms, 372 bonds, 54 residues, 1 model selected

view matrix models #1,0.45679,-0.5223,-0.7201,116.11,0.84237,0.51416,0.16142,145.16,0.28594,-0.68032,0.67483,88.372

view matrix models #1,0.45679,-0.5223,-0.7201,114.24,0.84237,0.51416,0.16142,146.41,0.28594,-0.68032,0.67483,87.683

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide sel cartoons

select #1

369 atoms, 372 bonds, 54 residues, 1 model selected

view matrix models #2,1,0,0,0.65788,0,1,0,0.30648,0,0,1,0.70826

view matrix models #2,1,0,0,-0.65234,0,1,0,1.2309,0,0,1,0.14732

save "/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs"

——— End of log from Tue Dec 20 17:39:04 2022 ———

opened ChimeraX session

show #1.1 models

show #2.2 models

hide #2.2 models

hide #2.1 models

show #2.1 models

hide #1.1 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

show sel cartoons

select #2:FeS

4 atoms, 4 bonds, 1 residue, 1 model selected

show sel atoms

style sel sphere

Changed 4 atom styles

select #2:FS4

Nothing selected

select #2:SF4

24 atoms, 36 bonds, 3 residues, 1 model selected

show sel atoms

style sel sphere

Changed 24 atom styles

surface #2 enclose /C-D

select add #2.3

1768 atoms, 36 bonds, 226 residues, 1 model selected

coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
6yez #2/D LEU 211 OXT

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30, maximum 9.66
Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16, maximum 13.86
To also show corresponding color key, enter the above coulombic command and add key true

surface #2 enclose /E

select add #2.5

2296 atoms, 36 bonds, 292 residues, 3 models selected

select subtract #2.4

1164 atoms, 36 bonds, 149 residues, 4 models selected

select subtract #2.3

552 atoms, 36 bonds, 69 residues, 3 models selected

coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
6yez #2/E LYS 129 OXT

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for Surface /E #2.5: minimum, -13.31, mean 0.69, maximum 9.65
To also show corresponding color key, enter the above coulombic command and add key true

show #2.2 models

hide #!1 models

select add #2.4

1684 atoms, 36 bonds, 212 residues, 2 models selected

select subtract #2.5

1156 atoms, 36 bonds, 146 residues, 3 models selected

transparency (#!2 & sel) 60

transparency (#!2 & sel) 0

select subtract #2.4

24 atoms, 36 bonds, 3 residues, 2 models selected

select add #2.3

636 atoms, 36 bonds, 83 residues, 1 model selected

transparency (#!2 & sel) 60

ui tool show AlphaFold

alphafold match Q8KCZ6

Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using UniProt identifier: Q8KCZ6 (UniProt Q8KCZ6)

Sequence Similarity
AlphaFold Model	Query Sequence	Identity %	Coverage %
Q8KCZ6	Q8KCZ6	100.0	100.0

Opened 1 AlphaFold model

rename #3 "AlphaFold Q8KCZ6 CbFdx"

Fetching A1Z1D6 UniProt info from https://www.uniprot.org/uniprot/A1Z1D6.xml

alphafold match A1Z1D6

Fetching compressed AlphaFold A1Z1D6 from https://alphafold.ebi.ac.uk/files/AF-A1Z1D6-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: A1Z1D6 (UniProt A1Z1D6)

Sequence Similarity
AlphaFold Model	Query Sequence	Identity %	Coverage %
A1Z1D6	A1Z1D6	100.0	100.0

Opened 1 AlphaFold model

rename #1 "AlphaFold A1Z1D6 PshB"

close #4

ui tool show Matchmaker

matchmaker #3 to #1

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker AlphaFold A1Z1D6 PshB, chain A (#1) with AlphaFold Q8KCZ6 CbFdx, chain A (#3), sequence alignment score = 92.4
RMSD between 42 pruned atom pairs is 0.750 angstroms; (across all 54 pairs: 3.659)

hide #2.2 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide sel cartoons

show #!1 models

select #3:cys

54 atoms, 45 bonds, 9 residues, 1 model selected

show sel atoms

color sel byhetero

hide #!2 models

show #!2 models

save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs"

——— End of log from Sun Sep 3 20:15:18 2023 ———

opened ChimeraX session

select #2/A:562-593

238 atoms, 243 bonds, 32 residues, 1 model selected

select #2/A:417-442,562-593

466 atoms, 475 bonds, 58 residues, 1 model selected

select #2/A:417-442,562-595

485 atoms, 496 bonds, 60 residues, 1 model selected

select #2/A:16-73,417-442,562-595

959 atoms, 986 bonds, 118 residues, 1 model selected

select #2/A:16-73,417-442,562-595,695-729

1238 atoms, 1272 bonds, 153 residues, 1 model selected

select #2/A:16-73,320-354,417-442,562-595,695-729

1512 atoms, 1555 bonds, 188 residues, 1 model selected

surface #2 enclose #2/A:16-73,320-354,417-442,562-595,695-729

close #2.6

surface #2 enclose #2/A:16-73,191-200,320-354,417-442,562-595,695-729

select subtract #2.6

1 model selected

close #2.6

surface #2 enclose #2/A:16-73,191-200,315-354,417-442,562-595,695-729

hide #2.3 models

hide #2.4 models

hide #2.5 models

select #2/B:2-41

327 atoms, 336 bonds, 40 residues, 1 model selected

select #2/B:2-41,172-176,291-331

693 atoms, 710 bonds, 86 residues, 1 model selected

select #2/B:2-41,172-176,291-331,392-421

945 atoms, 967 bonds, 116 residues, 1 model selected

select #2/B:2-41,172-176,291-331,392-423

959 atoms, 981 bonds, 118 residues, 1 model selected

select #2/B:2-41,172-176,291-331,392-419

929 atoms, 950 bonds, 114 residues, 1 model selected

select #2/B:2-41,172-176,291-331,392-420

935 atoms, 956 bonds, 115 residues, 1 model selected

select #2/B:2-41,172-176,291-331,392-420,535-573

1221 atoms, 1249 bonds, 154 residues, 1 model selected

select #2/B:2-41,172-176,291-331,392-420,535-575

1234 atoms, 1262 bonds, 156 residues, 1 model selected

select #2/B:2-44,172-176,291-331,392-420,535-575

1263 atoms, 1292 bonds, 159 residues, 1 model selected

select #2/B:2-44,162-176,291-331,392-420,535-575

1345 atoms, 1378 bonds, 169 residues, 1 model selected

select #2/B:2-44,162-176,291-331,392-420,535-575,666-705

1684 atoms, 1728 bonds, 209 residues, 1 model selected

select #2/B:2-44,162-176,291-331,392-420,535-575,665-707

1711 atoms, 1755 bonds, 212 residues, 1 model selected

surface #2 enclose #2/B:2-44,162-176,291-331,392-420,535-575,665-707

show #2.5 models

show #2.4 models

show #2.3 models

show #2.2 models

hide #2.2 models

select subtract #2.7

1 model selected

select add #2.7

1711 atoms, 212 residues, 1 model selected

coulombic sel

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_B SES surface #2.7: minimum, -15.22, mean -0.70, maximum 13.28
To also show corresponding color key, enter the above coulombic command and add key true

select subtract #2.7

1 model selected

select add #2.6

1649 atoms, 203 residues, 1 model selected

coulombic sel

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_A SES surface #2.6: minimum, -15.63, mean -1.25, maximum 12.20
To also show corresponding color key, enter the above coulombic command and add key true

select subtract #2.6

1 model selected

hide #!1 models

hide #3 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

show sel cartoons

show #2.2 models

select subtract #2.2

4 atoms, 4 bonds, 1 residue, 2 models selected

select add #2.2

728 atoms, 4 bonds, 98 residues, 1 model selected

coulombic sel

Coulombic values for 6yez_N SES surface #2.2: minimum, -22.35, mean -7.76, maximum 6.07
To also show corresponding color key, enter the above coulombic command and add key true

select subtract #2.2

4 atoms, 4 bonds, 1 residue, 2 models selected

select add #2.2

728 atoms, 4 bonds, 98 residues, 1 model selected

transparency (#!2 & sel) 30

hide #2.2 models

hide #2.3 models

select #2/N:FES@FE1/C:3003@FE1

2 atoms, 2 residues, 1 model selected

ui tool show Distances

distance style radius 0.3

[Repeated 2 time(s)]

distance style dashes 8

[Repeated 2 time(s)]

distance style dashes 7

[Repeated 2 time(s)]

distance style dashes 6

[Repeated 2 time(s)]

distance style color #00f900

[Repeated 2 time(s)]

distance #2/C:3003@FE1 #2/N:101@FE1

Distance between 6yez #2/C SF4 3003 FE1 and /N FES 101 FE1: 9.664Å

show #2.2 models

show #2.3 models

hide #2.5 models

show #2.5 models

save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs"

select #2:CL1,CLA

8357 atoms, 8921 bonds, 564 pseudobonds, 141 residues, 2 models selected

select #2:CL1

Nothing selected

select #2:CHL

802 atoms, 862 bonds, 60 pseudobonds, 15 residues, 2 models selected

select #2:CHL

802 atoms, 862 bonds, 60 pseudobonds, 15 residues, 2 models selected

show sel atoms

hide sel atoms

select #2/A-B:CHL

Nothing selected

select #2/A-B:CL0

65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected

show sel atoms

select #2/A-B:CL0,CLA

5318 atoms, 5662 bonds, 344 pseudobonds, 86 residues, 2 models selected

show sel atoms

color (#!2 & sel) forest green

color sel byhetero

save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs"

——— End of log from Sun Sep 3 20:48:37 2023 ———

opened ChimeraX session

select #2/A &~:16-73,191-200,315-354,417-442,562-595,695-729

7373 atoms, 7698 bonds, 180 pseudobonds, 597 residues, 2 models selected

select #2/A &~:16-73,191-200,315-354,417-442,562-595,695-729,SF4

7365 atoms, 7686 bonds, 180 pseudobonds, 596 residues, 2 models selected

delete atoms (#!2 & sel)

delete bonds (#!2 & sel)

select #2/B &~:2-44,162-176,291-331,392-420,535-575,665-707

7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected

select #2/B &~:2-44,162-176,291-331,392-420,535-575,665-707,SF4

7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected

select #2/B &~:2-44,162-176,291-331,392-420,535-575,665-707

7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected

delete atoms (#!2 & sel)

delete bonds (#!2 & sel)

select #2 &~/A-E/N

18189 atoms, 18861 bonds, 305 pseudobonds, 1703 residues, 2 models selected

delete atoms (#!2 & sel)

delete bonds (#!2 & sel)

hide #2.3 models

hide #2.4 models

hide #2.5 models

hide #2.6 models

hide #2.7 models

show #2.3 models

show #2.4 models

show #2.5 models

show #2.6 models

select add #2.6

1649 atoms, 203 residues, 1 model selected

coulombic sel

Coulombic values for 6yez_A SES surface #2.6: minimum, -23.39, mean -1.01, maximum 11.65
To also show corresponding color key, enter the above coulombic command and add key true

select subtract #2.6

1 model selected

show #2.7 models

select add #2.7

1711 atoms, 212 residues, 1 model selected

coulombic sel

Coulombic values for 6yez_B SES surface #2.7: minimum, -15.05, mean 0.76, maximum 12.84
To also show corresponding color key, enter the above coulombic command and add key true

save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI PetF truncated.pdb" models #2

save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs"

——— End of log from Sun Sep 3 21:12:02 2023 ———

opened ChimeraX session

hide #2.8 models

show #2.8 models

hide #2.7 models

hide #2.6 models

hide #2.5 models

hide #2.4 models

hide #2.3 models

hide #2.2 models

open 2fdn

2fdn title:
2[4FE-4S] ferredoxin from clostridium acidi-urici [more info...]

Chain information for 2fdn #5
Chain	Description	UniProt
A	FERREDOXIN	FER_CLOAC 1-55

Non-standard residues in 2fdn #5
SF4 — iron/sulfur cluster

Align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2

Unknown command: Align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2

help help:user

align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2

RMSD between 4 atom pairs is 0.181 angstroms

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide sel cartoons

show sel cartoons

ui tool show "Show Sequence Viewer"

sequence chain #2/A

Alignment identifier is 2/A

sequence chain #2/B

Alignment identifier is 2/B

select #sel #2/A

Expected an objects specifier or a keyword

select #2/A

1657 atoms, 1709 bonds, 7 pseudobonds, 204 residues, 3 models selected

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs"

——— End of log from Fri May 17 13:23:40 2024 ———

opened ChimeraX session

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI_IsiB_noFld.pdb"

Chain information for PSI_IsiB_noFld.pdb #6
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #!6 to #2 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6yez, chain D (#2) with PSI_IsiB_noFld.pdb, chain A (#6), sequence alignment score = 488.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6yez #2/D, PSI_IsiB_noFld.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 126 pruned atom pairs is 0.707 angstroms; (across all 142 pairs: 5.251)

hide #!6 models

show #!1 models

select #2/A:16-73,191-200,315-354,417-442,562-595,695-729

1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected

select #2/B

1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected

select #2/B:2-44,162-176,291-331,392-420,535-575,665-707

1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected

select #2/A:16-73,191-200,315-354,417-442,562-595,695-729

1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_0.pdb"

Chain information for PSI_6yez_A_B_for_docking_0.pdb #7
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #7 to #2 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_0.pdb, chain A (#7), sequence alignment score = 572.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6yez #2/B, PSI_6yez_A_B_for_docking_0.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 211 pruned atom pairs is 0.247 angstroms; (across all 211 pairs: 0.247)

matchmaker #7 to #2 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_0.pdb, chain A (#7), sequence alignment score = 572.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 6yez #2/B, PSI_6yez_A_B_for_docking_0.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 211 pruned atom pairs is 0.247 angstroms; (across all 211 pairs: 0.247)

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

select #2/A:73,191,200,315,354,417,442,562,595,695,729

108 atoms, 105 bonds, 5 pseudobonds, 11 residues, 2 models selected

color (#!2 & sel) yellow

select #2/B:44,162,176,291,331,392,420,535,575,665,707

90 atoms, 81 bonds, 5 pseudobonds, 11 residues, 2 models selected

color (#!2 & sel) yellow

hide #7 models

select #2/B:707

8 atoms, 7 bonds, 1 residue, 1 model selected

color (#!2 & sel) hot pink

select #2/B:2

5 atoms, 4 bonds, 1 residue, 1 model selected

color (#!2 & sel) blue

select #2/A:729/B:2

14 atoms, 12 bonds, 2 residues, 1 model selected

select #2/A:729

9 atoms, 8 bonds, 1 residue, 1 model selected

color (#!2 & sel) magenta

close #7

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_hike6_0.pdb"

Chain information for PSI_6yez_A_B_for_docking_hike6_0.pdb #7
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #7 to #2

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_hike6_0.pdb, chain A (#7), sequence alignment score = 551.5
RMSD between 211 pruned atom pairs is 0.251 angstroms; (across all 212 pairs: 0.314)

select #2/A-B:CYS

24 atoms, 20 bonds, 4 residues, 1 model selected

show sel atoms

style sel stick

Changed 24 atom styles

color sel byhetero

select #7/A-B:CYS

16 atoms, 12 bonds, 4 residues, 1 model selected

show sel atoms

[Repeated 1 time(s)]

select #7/A-B:CYS

16 atoms, 12 bonds, 4 residues, 1 model selected

hide #!2 models

show sel atoms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs"

——— End of log from Fri May 17 15:09:06 2024 ———

opened ChimeraX session

hide #!1 models

show #!2 models

hide #!4 models

hide #!5 models

combine #2#7

Remapping chain ID 'A' in PSI_6yez_A_B_for_docking_hike6_0.pdb #7 to 'F'

combine #2#7

Remapping chain ID 'A' in PSI_6yez_A_B_for_docking_hike6_0.pdb #7 to 'F'

select #8/F

1916 atoms, 1915 bonds, 479 residues, 1 model selected

select #8/F:GLY

392 atoms, 350 bonds, 98 residues, 1 model selected

help help:user

select sequence GGG

768 atoms, 735 bonds, 192 residues, 3 models selected

select sequence GGG|sequence GGGGG

Expected a keyword

select sequence GGG | GGGGG

Expected a keyword

select sequence GGGGG

480 atoms, 471 bonds, 120 residues, 3 models selected

ui tool show "Show Sequence Viewer"

sequence chain #8/F

Alignment identifier is 8/F

select #8/F:181-185,221-250,432-436

160 atoms, 157 bonds, 40 residues, 1 model selected

select sequence GGG

768 atoms, 735 bonds, 192 residues, 3 models selected

close #8-9

close #7

show #!5 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide sel atoms

hide sel cartoons

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

show sel cartoons

select #2/N:FES

4 atoms, 4 bonds, 1 residue, 1 model selected

show sel atoms

style sel stick

Changed 4 atom styles

style sel ball

Changed 4 atom styles

select #2/N:FES :<2 &/N:CYS

Nothing selected

select #2/N:FES :<2.5 &/N:CYS

18 atoms, 15 bonds, 3 residues, 1 model selected

select #2/N:FES :<2.8 &/N:CYS

24 atoms, 20 bonds, 4 residues, 1 model selected

show sel atoms

select #2/N :<4.5 &#2/A-E

106 atoms, 95 bonds, 12 residues, 1 model selected

show sel atoms

style sel stick

Changed 106 atom styles

color sel byhetero

select #2/A-E :<4.5 &#2/N

141 atoms, 134 bonds, 18 residues, 1 model selected

style sel stick

Changed 141 atom styles

show sel atoms

color sel byhetero

ui tool show H-Bonds

hbonds sel dashes 6 intraMol false intraRes false reveal true retainCurrent true log true

Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	1 AlphaFold A1Z1D6 PshB
	2 6yez
	3 AlphaFold Q8KCZ6 CbFdx
	5 2fdn
	6 PSI_IsiB_noFld.pdb

61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
AlphaFold A1Z1D6 PshB #1/A TYR 3 OH    6yez #2/N ASP 26 OD2                  no hydrogen          3.274  N/A
AlphaFold A1Z1D6 PshB #1/A THR 6 OG1   6yez #2/N GLN 58 OE1                  no hydrogen          2.570  N/A
AlphaFold A1Z1D6 PshB #1/A CYS 12 SG   6yez #2/N GLY 61 O                    no hydrogen          3.429  N/A
AlphaFold A1Z1D6 PshB #1/A CYS 20 SG   6yez #2/N SER 38 O                    no hydrogen          2.641  N/A
AlphaFold A1Z1D6 PshB #1/A THR 33 N    6yez #2/N SER 45 O                    no hydrogen          2.919  N/A
AlphaFold A1Z1D6 PshB #1/A THR 33 OG1  6yez #2/N SER 45 O                    no hydrogen          2.129  N/A
AlphaFold A1Z1D6 PshB #1/A LYS 45 NZ   6yez #2/N ALA 41 O                    no hydrogen          3.560  N/A
6yez #2/A ARG 42 NH1                   6yez #2/N GLN 58 O                    no hydrogen          3.483  N/A
6yez #2/A LYS 46 NZ                    6yez #2/N GLY 61 O                    no hydrogen          3.235  N/A
6yez #2/C LYS 35 NZ                    6yez #2/N TYR 37 OH                   no hydrogen          2.696  N/A
6yez #2/E ARG 106 NH2                  6yez #2/N ASP 26 OD1                  no hydrogen          3.124  N/A
6yez #2/E THR 117 OG1                  6yez #2/N ARG 40 O                    no hydrogen          3.442  N/A
6yez #2/N ASP 26 N                     AlphaFold A1Z1D6 PshB #1/A TYR 3 OH   no hydrogen          3.023  N/A
6yez #2/N TYR 37 OH                    2fdn #5/A HOH 179 O                   no hydrogen          1.912  N/A
6yez #2/N CYS 39 SG                    AlphaFold Q8KCZ6 CbFdx #3/A GLU 16 O  no hydrogen          3.985  N/A
6yez #2/N ARG 40 NE                    2fdn #5/A GLU 15 OE1                  no hydrogen          1.468  N/A
6yez #2/N ARG 40 NH1                   AlphaFold Q8KCZ6 CbFdx #3/A ASN 39 O  no hydrogen          3.073  N/A
6yez #2/N ARG 40 NH2                   AlphaFold Q8KCZ6 CbFdx #3/A ALA 45 O  no hydrogen          3.441  N/A
6yez #2/N SER 43 OG                    AlphaFold A1Z1D6 PshB #1/A CYS 19 O   no hydrogen          3.491  N/A
6yez #2/N CYS 44 SG                    AlphaFold A1Z1D6 PshB #1/A CYS 19 O   no hydrogen          3.519  N/A
6yez #2/N CYS 44 SG                    AlphaFold Q8KCZ6 CbFdx #3/A CYS 19 O  no hydrogen          3.157  N/A
6yez #2/N SER 45 OG                    2fdn #5/A HOH 131 O                   no hydrogen          3.265  N/A
6yez #2/N GLN 58 N                     2fdn #5/A HOH 143 O                   no hydrogen          2.715  N/A
6yez #2/N GLN 58 N                     2fdn #5/A HOH 157 O                   no hydrogen          3.070  N/A
6yez #2/N SER 59 N                     2fdn #5/A HOH 169 O                   no hydrogen          2.977  N/A
6yez #2/N THR 96 OG1                   2fdn #5/A HOH 131 O                   no hydrogen          2.408  N/A
6yez #2/N THR 96 OG1                   2fdn #5/A HOH 147 O                   no hydrogen          3.427  N/A
AlphaFold Q8KCZ6 CbFdx #3/A THR 6 OG1  6yez #2/N GLN 58 OE1                  no hydrogen          2.737  N/A
AlphaFold Q8KCZ6 CbFdx #3/A CYS 12 SG  6yez #2/N GLY 61 O                    no hydrogen          3.245  N/A
AlphaFold Q8KCZ6 CbFdx #3/A ASP 34 N   6yez #2/N SER 45 O                    no hydrogen          2.864  N/A
AlphaFold Q8KCZ6 CbFdx #3/A CYS 41 SG  6yez #2/N ARG 40 O                    no hydrogen          2.641  N/A
2fdn #5/A SER 10 OG (alt loc A)        6yez #2/N TYR 37 O                    no hydrogen          0.740  N/A
2fdn #5/A CYS 11 SG                    6yez #2/N SER 43 OG                   no hydrogen          3.518  N/A
2fdn #5/A GLU 15 N                     6yez #2/N ARG 40 O                    2fdn #5/A GLU 15 H   2.748  2.059
2fdn #5/A SER 25 OG (alt loc B)        6yez #2/N TYR 37 OH                   no hydrogen          2.248  N/A
2fdn #5/A TYR 30 OH                    6yez #2/N SER 38 O                    2fdn #5/A TYR 30 HH  3.238  2.616
2fdn #5/A CYS 47 SG                    6yez #2/N CYS 44 O                    no hydrogen          1.073  N/A
2fdn #5/A HOH 114 O                    6yez #2/N ILE 69 O                    no hydrogen          2.944  N/A
2fdn #5/A HOH 115 O                    6yez #2/N ALA 41 O                    no hydrogen          2.833  N/A
2fdn #5/A HOH 118 O                    6yez #2/N PHE 63 O                    no hydrogen          2.570  N/A
2fdn #5/A HOH 119 O                    6yez #2/N GLN 58 O                    no hydrogen          2.512  N/A
2fdn #5/A HOH 131 O                    6yez #2/N SER 45 OG                   no hydrogen          3.265  N/A
2fdn #5/A HOH 131 O                    6yez #2/N THR 96 OG1                  no hydrogen          2.408  N/A
2fdn #5/A HOH 138 O                    6yez #2/N TYR 37 O                    no hydrogen          3.553  N/A
2fdn #5/A HOH 139 O                    6yez #2/N GLY 61 O                    no hydrogen          1.926  N/A
2fdn #5/A HOH 141 O                    6yez #2/N ARG 40 O                    no hydrogen          2.648  N/A
2fdn #5/A HOH 147 O                    6yez #2/N THR 96 OG1                  no hydrogen          3.427  N/A
2fdn #5/A HOH 148 O                    6yez #2/N GLN 58 OE1                  no hydrogen          2.593  N/A
2fdn #5/A HOH 153 O                    6yez #2/N GLN 58 O                    no hydrogen          1.710  N/A
2fdn #5/A HOH 154 O                    6yez #2/N SER 59 O                    no hydrogen          2.738  N/A
2fdn #5/A HOH 155 O                    6yez #2/N GLN 58 O                    no hydrogen          3.210  N/A
2fdn #5/A HOH 159 O                    6yez #2/N ASP 26 O                    no hydrogen          3.660  N/A
2fdn #5/A HOH 161 O                    6yez #2/N TYR 37 O                    no hydrogen          2.800  N/A
2fdn #5/A HOH 171 O                    6yez #2/N SER 38 O                    no hydrogen          2.044  N/A
2fdn #5/A HOH 179 O                    6yez #2/N TYR 37 OH                   no hydrogen          1.912  N/A
2fdn #5/A HOH 186 O                    6yez #2/N TYR 23 OH                   no hydrogen          2.883  N/A
2fdn #5/A HOH 190 O                    6yez #2/N GLN 58 OE1                  no hydrogen          2.133  N/A
2fdn #5/A HOH 190 O                    6yez #2/N ILE 69 O                    no hydrogen          2.801  N/A
2fdn #5/A HOH 194 O                    6yez #2/N ILE 69 O                    no hydrogen          3.081  N/A
PSI_IsiB_noFld.pdb #6/A LYS 28 NZ      6yez #2/N SER 59 O                    no hydrogen          2.762  N/A
PSI_IsiB_noFld.pdb #6/A LYS 28 NZ      6yez #2/N GLY 61 O                    no hydrogen          3.493  N/A

61 hydrogen bonds found

hbonds sel interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2 6yez

5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6yez #2/A ARG 42 NH1   6yez #2/N GLN 58 O    no hydrogen  3.483  N/A
6yez #2/A LYS 46 NZ    6yez #2/N GLY 61 O    no hydrogen  3.235  N/A
6yez #2/C LYS 35 NZ    6yez #2/N TYR 37 OH   no hydrogen  2.696  N/A
6yez #2/E ARG 106 NH2  6yez #2/N ASP 26 OD1  no hydrogen  3.124  N/A
6yez #2/E THR 117 OG1  6yez #2/N ARG 40 O    no hydrogen  3.442  N/A

5 hydrogen bonds found

select #2/A-E :<4.5 &#2/N

141 atoms, 134 bonds, 18 residues, 1 model selected

hbonds sel interModel false intraModel false intraMol false intraRes false reveal true log true

Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2 6yez

0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):

0 hydrogen bonds found

close #7

hbonds sel interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2 6yez

5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6yez #2/A ARG 42 NH1   6yez #2/N GLN 58 O    no hydrogen  3.483  N/A
6yez #2/A LYS 46 NZ    6yez #2/N GLY 61 O    no hydrogen  3.235  N/A
6yez #2/C LYS 35 NZ    6yez #2/N TYR 37 OH   no hydrogen  2.696  N/A
6yez #2/E ARG 106 NH2  6yez #2/N ASP 26 OD1  no hydrogen  3.124  N/A
6yez #2/E THR 117 OG1  6yez #2/N ARG 40 O    no hydrogen  3.442  N/A

5 hydrogen bonds found

hide #!5 models

ui tool show Contacts

select #2/A-E

5656 atoms, 5816 bonds, 21 pseudobonds, 707 residues, 3 models selected

contacts sel restrict #2/N distanceOnly 4.5 resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true

Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False

85 distances
        atom1                 atom2          distance
6yez #2/C LYS 35 NZ    6yez #2/N TYR 37 OH     2.696
6yez #2/E ARG 106 NH2  6yez #2/N ASP 26 OD1    3.124
6yez #2/C GLN 16 NE2   6yez #2/N CYS 44 CB     3.133
6yez #2/A LYS 46 NZ    6yez #2/N GLY 61 O      3.235
6yez #2/C ILE 12 CD1   6yez #2/N CYS 39 CA     3.319
6yez #2/C GLN 16 NE2   6yez #2/N CYS 44 CA     3.355
6yez #2/E ARG 106 NH1  6yez #2/N TYR 23 CE2    3.379
6yez #2/E THR 117 OG1  6yez #2/N ARG 40 O      3.442
6yez #2/C LYS 35 CG    6yez #2/N TYR 37 OH     3.473
6yez #2/A ARG 42 NH1   6yez #2/N GLN 58 O      3.483
6yez #2/A ARG 42 NH1   6yez #2/N ILE 69 CG1    3.526
6yez #2/C LYS 35 CD    6yez #2/N TYR 37 OH     3.585
6yez #2/C LYS 35 CE    6yez #2/N TYR 37 OH     3.650
6yez #2/A LYS 46 CE    6yez #2/N SER 59 O      3.708
6yez #2/C ILE 12 CD1   6yez #2/N CYS 39 N      3.715
6yez #2/C ILE 12 CD1   6yez #2/N SER 38 O      3.754
6yez #2/C CYS 14 CA    6yez #2/N SER 38 OG     3.781
6yez #2/A LYS 46 CD    6yez #2/N SER 59 O      3.788
6yez #2/C ILE 12 CD1   6yez #2/N CYS 39 CB     3.788
6yez #2/C GLN 16 NE2   6yez #2/N SER 45 N      3.796
6yez #2/E ARG 70 CZ    6yez #2/N GLU 30 OE2    3.802
6yez #2/A ARG 42 NH1   6yez #2/N ILE 69 CD1    3.805
6yez #2/E THR 117 OG1  6yez #2/N ALA 41 CB     3.818
6yez #2/A ARG 42 CZ    6yez #2/N ILE 69 CG1    3.820
6yez #2/E ARG 70 NH1   6yez #2/N GLU 30 OE2    3.841
6yez #2/C ILE 12 CD1   6yez #2/N SER 38 C      3.847
6yez #2/C CYS 14 CB    6yez #2/N SER 38 OG     3.922
6yez #2/C GLN 16 NE2   6yez #2/N SER 43 O      3.930
6yez #2/A LYS 46 CG    6yez #2/N SER 59 OG     3.975
6yez #2/A LYS 46 CB    6yez #2/N SER 59 OG     3.987
6yez #2/A ARG 42 NE    6yez #2/N ILE 69 CG1    3.994
6yez #2/E ARG 70 NE    6yez #2/N GLU 30 OE2    4.021
6yez #2/E THR 117 OG1  6yez #2/N ALA 41 CA     4.021
6yez #2/C LYS 35 NZ    6yez #2/N TYR 37 CZ     4.039
6yez #2/C GLN 16 NE2   6yez #2/N CYS 44 C      4.040
6yez #2/A LYS 46 CG    6yez #2/N SER 59 O      4.085
6yez #2/C GLN 16 CD    6yez #2/N CYS 44 CB     4.085
6yez #2/A ARG 42 CD    6yez #2/N GLU 70 OE1    4.097
6yez #2/E THR 117 OG1  6yez #2/N ARG 40 C      4.100
6yez #2/C GLN 16 OE1   6yez #2/N PHE 63 CE2    4.103
6yez #2/C GLN 16 OE1   6yez #2/N PHE 63 CZ     4.120
6yez #2/E ARG 106 CZ   6yez #2/N TYR 23 CE2    4.121
6yez #2/C ARG 19 NH1   6yez #2/N THR 96 CG2    4.133
6yez #2/C GLN 16 CG    6yez #2/N CYS 44 CB     4.147
6yez #2/C PRO 59 CG    6yez #2/N CYS 39 CB     4.148
6yez #2/C PRO 59 CB    6yez #2/N SER 43 OG     4.171
6yez #2/E ARG 106 NH1  6yez #2/N TYR 23 CD2    4.173
6yez #2/C LYS 35 CG    6yez #2/N TYR 37 CZ     4.175
6yez #2/A LYS 46 NZ    6yez #2/N SER 59 O      4.182
6yez #2/A ARG 42 NE    6yez #2/N ILE 69 CG2    4.190
6yez #2/C LYS 35 CB    6yez #2/N TYR 37 OH     4.190
6yez #2/C GLN 16 CD    6yez #2/N SER 43 O      4.191
6yez #2/E ARG 106 CZ   6yez #2/N ASP 26 OD1    4.192
6yez #2/C GLN 16 NE2   6yez #2/N PHE 63 CE2    4.196
6yez #2/A ARG 42 NH1   6yez #2/N GLN 58 CB     4.208
6yez #2/E ARG 70 NH2   6yez #2/N GLU 30 OE2    4.209
6yez #2/C ILE 12 O     6yez #2/N SER 38 CB     4.235
6yez #2/E ARG 106 NH1  6yez #2/N TYR 23 OH     4.249
6yez #2/A LYS 46 CG    6yez #2/N SER 59 CA     4.265
6yez #2/A LYS 46 CE    6yez #2/N GLY 61 O      4.269
6yez #2/A LYS 46 CE    6yez #2/N GLN 58 O      4.274
6yez #2/E ARG 106 NH1  6yez #2/N TYR 23 CZ     4.275
6yez #2/C CYS 14 CA    6yez #2/N SER 38 CB     4.277
6yez #2/E ARG 106 NH2  6yez #2/N TYR 23 CE2    4.281
6yez #2/E ARG 106 NH2  6yez #2/N ASP 26 CG     4.311
6yez #2/C GLN 16 CG    6yez #2/N SER 43 O      4.316
6yez #2/C GLN 16 CD    6yez #2/N PHE 63 CE2    4.327
6yez #2/C PRO 59 CB    6yez #2/N CYS 39 CB     4.328
6yez #2/C GLN 16 CD    6yez #2/N CYS 44 CA     4.366
6yez #2/A LYS 46 NZ    6yez #2/N GLY 61 C      4.370
6yez #2/C ILE 12 CB    6yez #2/N SER 38 O      4.393
6yez #2/A ARG 42 NE    6yez #2/N ILE 69 CB     4.406
6yez #2/E THR 117 OG1  6yez #2/N ALA 41 N      4.411
6yez #2/E ARG 70 NH2   6yez #2/N ASP 26 O      4.425
6yez #2/C LYS 35 CB    6yez #2/N TYR 37 CZ     4.438
6yez #2/E ARG 106 NH1  6yez #2/N ASP 26 OD1    4.440
6yez #2/A ARG 42 NE    6yez #2/N GLU 70 OE1    4.443
6yez #2/C LYS 35 CD    6yez #2/N TYR 37 CZ     4.447
6yez #2/E THR 117 CB   6yez #2/N ARG 40 O      4.448
6yez #2/C ILE 12 CD1   6yez #2/N CYS 39 C      4.449
6yez #2/A ARG 42 NH1   6yez #2/N GLN 58 C      4.456
6yez #2/C ILE 12 CG1   6yez #2/N SER 38 O      4.458
6yez #2/E VAL 115 CG2  6yez #2/N ALA 41 CB     4.473
6yez #2/A LYS 46 CE    6yez #2/N SER 59 CA     4.493
6yez #2/A LYS 46 CE    6yez #2/N SER 59 C      4.500

85 distances

show #!5 models

ui tool show "Show Sequence Viewer"

sequence chain #2/N

Alignment identifier is 2/N

select #2/N:23,26,30,37-45,58-63,96

142 atoms, 139 bonds, 19 residues, 1 model selected

show sel atoms

style sel stick

Changed 142 atom styles

color sel byhetero

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 19 items

help help:user

split #2 atoms /N

Split 6yez (#2) into 2 models

Chain information for 6yez 1 #2.1
Chain	Description
N	No description available

Chain information for 6yez 2 #2.2
Chain	Description
A	No description available
B	No description available
C	No description available
D	No description available
E	No description available

hide #!2.1 models

split #5:1-14

Did not split 2fdn, has only one piece

select #5:1-14

168 atoms, 168 bonds, 14 residues, 1 model selected

select #5:1-14,17-23,37-43

334 atoms, 333 bonds, 28 residues, 1 model selected

select #5:1-14,17-23,31-43

409 atoms, 408 bonds, 34 residues, 1 model selected

select #5:1-14,17-23,31-55

558 atoms, 559 bonds, 46 residues, 1 model selected

color sel medium blue

color sel byhetero

hide #!2 models

select #2/A-E :<4.5 &#5

178 atoms, 150 bonds, 39 residues, 1 model selected

select #2/A-E :<5 &#5

213 atoms, 181 bonds, 45 residues, 1 model selected

select #2/A-E :<3 &#5

98 atoms, 86 bonds, 16 residues, 1 model selected

select #2/A-E :<4 &#5

164 atoms, 140 bonds, 33 residues, 1 model selected

select #2/A-E :<4 &#5&~:HOH

144 atoms, 140 bonds, 13 residues, 1 model selected

select #2/A-E :<3 &#5&~:HOH

88 atoms, 86 bonds, 6 residues, 1 model selected

select #2/A-E :<2 &#5&~:HOH

35 atoms, 33 bonds, 2 residues, 1 model selected

select #2/A-E :<4 &#5&~:HOH

144 atoms, 140 bonds, 13 residues, 1 model selected

ui tool show Clashes

show #!2 models

clashes sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

10 clashes
        atom1                   atom2            overlap  distance
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 O     1.079    2.041
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C GLN 16 NE2   1.030    2.310
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 O     1.019    1.401
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C GLN 16 CG    0.900    2.680
2fdn #5/A ILE 9 HD12   6yez 2 #2.2/C GLN 16 NE2   0.839    1.801
2fdn #5/A CYS 11 HA    6yez 2 #2.2/C ILE 12 CD1   0.775    2.105
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 O     0.738    2.382
2fdn #5/A GLU 15 OE2   6yez 2 #2.2/E VAL 91 CG1   0.706    2.654
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 NE2   0.661    1.979
2fdn #5/A ILE 9 HD13   6yez 2 #2.2/C GLN 16 CG    0.632    2.248

10 clashes

select #5

762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 151 items

color sel byhetero

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"

select #5:12,14,16,91

31 atoms, 29 bonds, 3 residues, 1 model selected

select #5:9,11,15,49

60 atoms, 56 bonds, 4 residues, 1 model selected

hide sel atoms

show sel atoms

color sel orange

color sel byhetero

show #!2.1 models

hide #!5 models

show #!5 models

hide #!5 models

show #!5 models

hide #!2.2 models

show #!2.2 models

hide #!2.2 models

hide #!5 models

show #!5 models

hide #!5 models

show #!5 models

hide #!5 models

show #!5 models

show #!2.2 models

select #2/N:FES@FE1,FE2,S1,S2:44@SG

5 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/N:FES@FE1,FE2,S1,S2:44@SG:39@SG:47@SG:77@SG

8 atoms, 4 bonds, 4 pseudobonds, 5 residues, 2 models selected

style sel ball

Changed 8 atom styles

align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG toAtomsl #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG

Expected a keyword

align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG

RMSD between 8 atom pairs is 0.719 angstroms

close #7

select #2/A-E :<4 &#5&~:HOH

120 atoms, 118 bonds, 10 residues, 1 model selected

hide #!2 models

show #!2 models

select #5:1-55 :<4&#2/A-E

86 atoms, 80 bonds, 11 residues, 1 model selected

clashes sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

31 clashes
          atom1                    atom2          overlap  distance
6yez 2 #2.2/E ARG 106 CZ   2fdn #5/A HOH 183 O     2.185    0.885
6yez 2 #2.2/C ARG 19 CZ    2fdn #5/A HOH 149 O     1.833    1.237
6yez 2 #2.2/E ARG 106 NE   2fdn #5/A HOH 183 O     1.591    1.109
6yez 2 #2.2/E VAL 91 O     2fdn #5/A HOH 182 O     1.380    1.100
6yez 2 #2.2/E VAL 91 C     2fdn #5/A HOH 182 O     1.295    1.775
6yez 2 #2.2/C GLN 16 NE2   2fdn #5/A VAL 49 HG11   1.244    1.396
6yez 2 #2.2/C ARG 19 NH1   2fdn #5/A HOH 149 O     1.149    1.551
6yez 2 #2.2/C CYS 14 O     2fdn #5/A ILE 9 HG22    1.100    1.320
6yez 2 #2.2/C CYS 14 CB    2fdn #5/A ILE 9 HD11    1.095    1.785
6yez 2 #2.2/C CYS 14 O     2fdn #5/A ILE 9 CG2     1.094    2.026
6yez 2 #2.2/C CYS 14 CB    2fdn #5/A ILE 9 CD1     1.091    2.489
6yez 2 #2.2/E ARG 106 CD   2fdn #5/A HOH 183 O     1.078    2.262
6yez 2 #2.2/C ARG 19 NE    2fdn #5/A HOH 117 O     1.078    1.622
6yez 2 #2.2/C CYS 14 CA    2fdn #5/A ILE 9 HB      1.036    1.844
6yez 2 #2.2/C GLN 16 NE2   2fdn #5/A VAL 49 CG1    1.032    2.308
6yez 2 #2.2/E ARG 106 NH2  2fdn #5/A HOH 183 O     1.015    1.685
6yez 2 #2.2/C ARG 19 NE    2fdn #5/A HOH 149 O     0.963    1.737
6yez 2 #2.2/E VAL 91 CG1   2fdn #5/A HOH 182 O     0.944    2.396
6yez 2 #2.2/C CYS 14 CA    2fdn #5/A ILE 9 CB      0.919    2.661
6yez 2 #2.2/E VAL 91 CA    2fdn #5/A HOH 182 O     0.915    2.425
6yez 2 #2.2/C ILE 12 CD1   2fdn #5/A CYS 11 HA     0.873    2.007
6yez 2 #2.2/C ARG 19 CD    2fdn #5/A HOH 149 O     0.871    2.469
6yez 2 #2.2/E ARG 106 NH1  2fdn #5/A HOH 183 O     0.810    1.890
6yez 2 #2.2/C ARG 19 CZ    2fdn #5/A HOH 117 O     0.807    2.263
6yez 2 #2.2/C CYS 14 CB    2fdn #5/A ILE 9 CG1     0.774    2.806
6yez 2 #2.2/C CYS 14 O     2fdn #5/A ILE 9 CB      0.742    2.378
6yez 2 #2.2/C CYS 14 O     2fdn #5/A ILE 9 CD1     0.695    2.425
6yez 2 #2.2/C CYS 14 CA    2fdn #5/A ILE 9 CG1     0.683    2.897
6yez 2 #2.2/C CYS 14 CA    2fdn #5/A ILE 9 HD11    0.668    2.212
6yez 2 #2.2/C CYS 14 CA    2fdn #5/A ILE 9 CD1     0.667    2.913
6yez 2 #2.2/C GLN 16 NE2   2fdn #5/A PRO 48 CG     0.613    2.727

31 clashes

close #7

select #5:1-55

652 atoms, 657 bonds, 55 residues, 1 model selected

clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

16 clashes
        atom1                   atom2            overlap  distance
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 NE2   1.244    1.396
2fdn #5/A ILE 9 HG22   6yez 2 #2.2/C CYS 14 O     1.100    1.320
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CB    1.095    1.785
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 O     1.094    2.026
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CB    1.091    2.489
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 CA    1.036    1.844
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 NE2   1.032    2.308
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 CA    0.919    2.661
2fdn #5/A CYS 11 HA    6yez 2 #2.2/C ILE 12 CD1   0.873    2.007
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CB    0.774    2.806
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 O     0.742    2.378
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 O     0.695    2.425
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CA    0.683    2.897
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CA    0.668    2.212
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CA    0.667    2.913
2fdn #5/A PRO 48 CG    6yez 2 #2.2/C GLN 16 NE2   0.613    2.727

16 clashes

select #5:9,11,48-49

59 atoms, 57 bonds, 4 residues, 1 model selected

align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA:77@SG

RMSD between 10 atom pairs is 0.673 angstroms

select #5:1-55

652 atoms, 657 bonds, 55 residues, 1 model selected

clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

15 clashes
        atom1                   atom2            overlap  distance
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 NE2   1.558    1.082
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CB    1.548    1.332
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CB    1.462    2.118
2fdn #5/A ILE 9 HG22   6yez 2 #2.2/C CYS 14 O     1.448    0.972
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 NE2   1.337    2.003
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 O     1.287    1.833
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 CA    1.254    1.626
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 CA    1.171    2.409
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CB    1.000    2.580
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CA    0.871    2.709
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CA    0.845    2.035
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CA    0.807    2.773
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 SG    0.730    2.040
2fdn #5/A CYS 11 HA    6yez 2 #2.2/C ILE 12 CD1   0.693    2.187
2fdn #5/A PRO 48 HB2   6yez 2 #2.2/C GLN 16 CD    0.623    1.987

15 clashes

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 98 items

hide #!2.2 models

align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA,C:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA,C:77@SG

RMSD between 11 atom pairs is 0.654 angstroms

select #5:1-55

652 atoms, 657 bonds, 55 residues, 1 model selected

clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

0 clashes
atom1  atom2  overlap  distance

No clashes

show #!2.2 models

clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

No atoms match given atom specifier

select #5:1-55

652 atoms, 657 bonds, 55 residues, 1 model selected

clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

14 clashes
        atom1                   atom2            overlap  distance
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 NE2   1.670    0.970
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CB    1.590    1.290
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CB    1.488    2.092
2fdn #5/A ILE 9 HG22   6yez 2 #2.2/C CYS 14 O     1.470    0.950
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 NE2   1.451    1.889
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 O     1.311    1.809
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 CA    1.236    1.644
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 CA    1.157    2.423
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CB    0.994    2.586
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CA    0.873    2.707
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CA    0.853    2.027
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CA    0.794    2.786
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 SG    0.743    2.027
2fdn #5/A CYS 11 HA    6yez 2 #2.2/C ILE 12 CD1   0.649    2.231

14 clashes

hide #!5 models

show #!5 models

hide #!5 models

show #!5 models

align #5:11@CB,CA,C:14 toAtoms #2/N:39@CB,CA,C

Unequal number of atoms to pair, 13 and 3

align #5:11@CB,CA,C toAtoms #2/N:39@CB,CA,C

RMSD between 3 atom pairs is 0.032 angstroms

hide #!2.1 models

select #5:1-55

652 atoms, 657 bonds, 55 residues, 1 model selected

clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True

40 clashes
        atom1                   atom2            overlap  distance
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 NE2   2.426    0.914
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 O     2.354    0.766
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 NE2   2.183    0.457
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 CA    2.131    0.749
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 CA    1.896    1.684
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 CD    1.861    1.449
2fdn #5/A ILE 9 HG23   6yez 2 #2.2/C CYS 14 O     1.757    0.663
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 CD    1.639    0.971
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 C     1.597    1.713
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CB    1.539    2.041
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 CB    1.513    2.067
2fdn #5/A VAL 49 CB    6yez 2 #2.2/C GLN 16 NE2   1.500    1.840
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 CB    1.492    2.088
2fdn #5/A ILE 9 HG22   6yez 2 #2.2/C CYS 14 O     1.464    0.956
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 CB    1.369    1.511
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 SG    1.353    1.417
2fdn #5/A ILE 9 HD11   6yez 2 #2.2/C CYS 14 CB    1.336    1.544
2fdn #5/A VAL 49 HG12  6yez 2 #2.2/C GLN 16 NE2   1.275    1.365
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 OE1   1.226    1.894
2fdn #5/A ILE 9 CG2    6yez 2 #2.2/C CYS 14 CA    1.180    2.400
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 C     1.152    2.158
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C CYS 14 SG    1.135    2.335
2fdn #5/A VAL 49 HG13  6yez 2 #2.2/C GLN 16 OE1   1.118    1.302
2fdn #5/A ILE 9 CB     6yez 2 #2.2/C CYS 14 O     1.081    2.039
2fdn #5/A ILE 9 HG23   6yez 2 #2.2/C CYS 14 C     1.052    1.558
2fdn #5/A ILE 9 HG22   6yez 2 #2.2/C CYS 14 C     1.047    1.563
2fdn #5/A VAL 49 HG13  6yez 2 #2.2/C GLN 16 CD    1.029    1.581
2fdn #5/A ILE 9 CD1    6yez 2 #2.2/C GLN 16 CG    1.005    2.575
2fdn #5/A ILE 9 HD12   6yez 2 #2.2/C GLN 16 CG    0.986    1.894
2fdn #5/A VAL 49 CG2   6yez 2 #2.2/C GLN 16 NE2   0.921    2.419
2fdn #5/A VAL 49 HG13  6yez 2 #2.2/C GLN 16 NE2   0.893    1.747
2fdn #5/A ILE 9 HG21   6yez 2 #2.2/C CYS 14 O     0.882    1.538
2fdn #5/A ILE 9 CG1    6yez 2 #2.2/C CYS 14 CA    0.881    2.699
2fdn #5/A ILE 9 CA     6yez 2 #2.2/C CYS 14 CA    0.878    2.702
2fdn #5/A ILE 9 HG13   6yez 2 #2.2/C CYS 14 CB    0.821    2.059
2fdn #5/A VAL 49 HG12  6yez 2 #2.2/C GLN 16 CD    0.810    1.800
2fdn #5/A ILE 9 HB     6yez 2 #2.2/C CYS 14 C     0.800    1.810
2fdn #5/A VAL 49 CG1   6yez 2 #2.2/C GLN 16 CG    0.772    2.808
2fdn #5/A VAL 49 CA    6yez 2 #2.2/C GLN 16 NE2   0.683    2.657
2fdn #5/A VAL 49 HG11  6yez 2 #2.2/C GLN 16 CG    0.683    2.197

40 clashes

select #5:9,49

35 atoms, 33 bonds, 2 residues, 1 model selected

hide sel atoms

show #!2.1 models

select #2/C:16

9 atoms, 8 bonds, 1 residue, 1 model selected

ui tool show H-Bonds

select #2/C:16|#5:1-55

661 atoms, 665 bonds, 17 pseudobonds, 56 residues, 3 models selected

select #2/C:16/N

737 atoms, 748 bonds, 4 pseudobonds, 99 residues, 3 models selected

hbonds sel restrict both interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2.1 6yez 1
	2.2 6yez 2

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 restrict both resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

19 contacts
          atom1                      atom2            overlap  distance
6yez 1 #2.1/N GLY 42 CA    6yez 1 #2.1/N FES 101 S2    0.389    3.261
6yez 1 #2.1/N CYS 44 SG    6yez 1 #2.1/N FES 101 FE1   0.123    2.277
6yez 1 #2.1/N FES 101 FE1  6yez 1 #2.1/N CYS 39 SG     0.081    2.319
6yez 1 #2.1/N FES 101 FE2  6yez 1 #2.1/N CYS 47 SG     0.040    2.360
6yez 1 #2.1/N CYS 44 O     6yez 1 #2.1/N FES 101 S2    -0.022    3.212
6yez 1 #2.1/N LEU 75 CD1   6yez 1 #2.1/N FES 101 S2    -0.065    3.715
6yez 1 #2.1/N CYS 44 N     6yez 1 #2.1/N FES 101 S2    -0.080    3.090
6yez 1 #2.1/N GLY 42 C     6yez 1 #2.1/N FES 101 S2    -0.102    3.482
6yez 1 #2.1/N CYS 44 CA    6yez 1 #2.1/N FES 101 S2    -0.180    3.830
6yez 1 #2.1/N CYS 77 SG    6yez 1 #2.1/N FES 101 FE2   -0.190    2.590
6yez 1 #2.1/N CYS 47 CB    6yez 1 #2.1/N FES 101 S1    -0.219    3.869
6yez 1 #2.1/N SER 43 N     6yez 1 #2.1/N FES 101 S2    -0.245    3.255
6yez 1 #2.1/N ARG 40 N     6yez 1 #2.1/N FES 101 S1    -0.246    3.256
6yez 1 #2.1/N LEU 75 CD2   6yez 1 #2.1/N FES 101 S2    -0.266    3.916
6yez 1 #2.1/N SER 38 N     6yez 1 #2.1/N FES 101 S1    -0.279    3.289
6yez 1 #2.1/N TYR 37 CB    6yez 1 #2.1/N FES 101 S1    -0.280    3.930
6yez 1 #2.1/N ARG 40 CA    6yez 1 #2.1/N FES 101 S1    -0.346    3.996
6yez 1 #2.1/N FES 101 S1   6yez 1 #2.1/N TYR 37 CA     -0.381    4.031
6yez 1 #2.1/N FES 101 S2   6yez 1 #2.1/N CYS 39 SG     -0.394    3.534

19 contacts

select #2/C:16/N

737 atoms, 748 bonds, 23 pseudobonds, 99 residues, 4 models selected

select #2/C:16

9 atoms, 8 bonds, 1 residue, 1 model selected

contacts sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

0 contacts
atom1  atom2  overlap  distance

No contacts

select #2/C:14

6 atoms, 5 bonds, 1 residue, 1 model selected

contacts sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

0 contacts
atom1  atom2  overlap  distance

No contacts

close #8

select #5:9,49

35 atoms, 33 bonds, 2 residues, 1 model selected

show sel atoms

hide #!2.1 models

show #!2.1 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

style sel stick

Changed 728 atom styles

color sel byhetero

ui tool show Contacts

contacts sel restrict #2/A-E resSeparation 5 interModel false intraMol false select true color #00f900 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

0 contacts
atom1  atom2  overlap  distance

No contacts

contacts sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true

No atoms match given atom specifier

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

contacts sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

0 contacts
atom1  atom2  overlap  distance

No contacts

select #2/N :<4.5 &#2/A-E

106 atoms, 95 bonds, 12 residues, 1 model selected

contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true

Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False

44 distances
         atom1                      atom2             distance
6yez 2 #2.2/C CYS 14 SG   6yez 2 #2.2/C SF4 3003 FE1    2.513
6yez 2 #2.2/C LYS 35 NZ   6yez 2 #2.2/E ASP 94 OD1      2.817
6yez 2 #2.2/C LYS 35 CE   6yez 2 #2.2/E ASP 94 OD1      3.169
6yez 2 #2.2/C LYS 35 NZ   6yez 2 #2.2/E ASP 94 CB       3.301
6yez 2 #2.2/C CYS 14 SG   6yez 2 #2.2/C SF4 3003 S2     3.328
6yez 2 #2.2/C CYS 14 N    6yez 2 #2.2/C SF4 3003 S3     3.398
6yez 2 #2.2/C LYS 35 NZ   6yez 2 #2.2/E ASP 94 CG       3.427
6yez 2 #2.2/C CYS 14 CB   6yez 2 #2.2/C SF4 3003 FE1    3.477
6yez 2 #2.2/C PRO 59 CD   6yez 2 #2.2/C SF4 3003 S2     3.547
6yez 2 #2.2/C CYS 14 N    6yez 2 #2.2/C SF4 3003 FE1    3.558
6yez 2 #2.2/C ILE 12 N    6yez 2 #2.2/C SF4 3003 S4     3.574
6yez 2 #2.2/C ARG 19 CZ   6yez 2 #2.2/D GLU 176 CB      3.741
6yez 2 #2.2/C PRO 59 CD   6yez 2 #2.2/C SF4 3003 FE1    3.759
6yez 2 #2.2/C ARG 19 NH1  6yez 2 #2.2/D GLU 176 CG      3.791
6yez 2 #2.2/C LYS 35 CE   6yez 2 #2.2/E ASP 94 CB       3.834
6yez 2 #2.2/C PRO 59 O    6yez 2 #2.2/E VAL 115 CG1     3.837
6yez 2 #2.2/C CYS 14 SG   6yez 2 #2.2/C SF4 3003 S3     3.855
6yez 2 #2.2/C ARG 19 NH1  6yez 2 #2.2/D GLU 176 CB      3.861
6yez 2 #2.2/C LYS 35 CE   6yez 2 #2.2/E ASP 94 CG       3.942
6yez 2 #2.2/C ARG 19 CG   6yez 2 #2.2/D GLU 176 CB      3.953
6yez 2 #2.2/C ARG 19 NH2  6yez 2 #2.2/D GLU 176 O       3.953
6yez 2 #2.2/C PRO 59 O    6yez 2 #2.2/E VAL 115 CG2     3.956
6yez 2 #2.2/C ARG 19 NH2  6yez 2 #2.2/D GLU 176 CB      3.961
6yez 2 #2.2/C CYS 14 CA   6yez 2 #2.2/C SF4 3003 FE1    3.964
6yez 2 #2.2/C ILE 12 CG1  6yez 2 #2.2/C SF4 3003 S4     3.982
6yez 2 #2.2/C ARG 19 NE   6yez 2 #2.2/D GLU 176 CB      4.078
6yez 2 #2.2/C LYS 35 CE   6yez 2 #2.2/E THR 99 CG2      4.085
6yez 2 #2.2/C PRO 59 CD   6yez 2 #2.2/C SF4 3003 FE3    4.085
6yez 2 #2.2/C PRO 59 CD   6yez 2 #2.2/C SF4 3003 S4     4.089
6yez 2 #2.2/C ARG 19 CZ   6yez 2 #2.2/D GLU 176 CG      4.095
6yez 2 #2.2/C CYS 14 C    6yez 2 #2.2/C SF4 3003 S3     4.143
6yez 2 #2.2/C ILE 12 N    6yez 2 #2.2/C SF4 3003 FE2    4.195
6yez 2 #2.2/C CYS 14 CA   6yez 2 #2.2/C SF4 3003 S3     4.198
6yez 2 #2.2/C ARG 19 NH2  6yez 2 #2.2/D GLU 176 CG      4.263
6yez 2 #2.2/C LYS 35 CG   6yez 2 #2.2/E ASP 94 OD1      4.284
6yez 2 #2.2/C LYS 35 CD   6yez 2 #2.2/E ASP 94 OD1      4.295
6yez 2 #2.2/C PRO 59 O    6yez 2 #2.2/E VAL 115 CB      4.335
6yez 2 #2.2/C CYS 14 C    6yez 2 #2.2/C SF4 3003 FE1    4.384
6yez 2 #2.2/C PRO 59 N    6yez 2 #2.2/C SF4 3003 S2     4.384
6yez 2 #2.2/C CYS 14 SG   6yez 2 #2.2/C SF4 3003 FE4    4.408
6yez 2 #2.2/C GLN 16 N    6yez 2 #2.2/C SF4 3003 S2     4.411
6yez 2 #2.2/C ILE 12 CG1  6yez 2 #2.2/C SF4 3003 FE1    4.414
6yez 2 #2.2/C PRO 59 CG   6yez 2 #2.2/C SF4 3003 FE1    4.463
6yez 2 #2.2/C ILE 12 CG2  6yez 2 #2.2/E ASN 119 ND2     4.478

44 distances

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true

Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False

0 distances
atom1  atom2  distance

No distances

close #8

close #6

close #3-4

close #1

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"

rename #2 id 1

rename #1 id 2

rename #5 id 1

rename #7 id 3

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"

combine #2.1#2.2

hide #!2 models

select #4/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

contacts sel restrict #4/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true

Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False

85 distances
           atom1                        atom2              distance
combination #4/N TYR 37 OH   combination #4/C LYS 35 NZ      2.696
combination #4/N ASP 26 OD1  combination #4/E ARG 106 NH2    3.124
combination #4/N CYS 44 CB   combination #4/C GLN 16 NE2     3.133
combination #4/N GLY 61 O    combination #4/A LYS 46 NZ      3.235
combination #4/N CYS 39 CA   combination #4/C ILE 12 CD1     3.319
combination #4/N CYS 44 CA   combination #4/C GLN 16 NE2     3.355
combination #4/N TYR 23 CE2  combination #4/E ARG 106 NH1    3.379
combination #4/N ARG 40 O    combination #4/E THR 117 OG1    3.442
combination #4/N TYR 37 OH   combination #4/C LYS 35 CG      3.473
combination #4/N GLN 58 O    combination #4/A ARG 42 NH1     3.483
combination #4/N ILE 69 CG1  combination #4/A ARG 42 NH1     3.526
combination #4/N TYR 37 OH   combination #4/C LYS 35 CD      3.585
combination #4/N TYR 37 OH   combination #4/C LYS 35 CE      3.650
combination #4/N SER 59 O    combination #4/A LYS 46 CE      3.708
combination #4/N CYS 39 N    combination #4/C ILE 12 CD1     3.715
combination #4/N SER 38 O    combination #4/C ILE 12 CD1     3.754
combination #4/N SER 38 OG   combination #4/C CYS 14 CA      3.781
combination #4/N SER 59 O    combination #4/A LYS 46 CD      3.788
combination #4/N CYS 39 CB   combination #4/C ILE 12 CD1     3.788
combination #4/N SER 45 N    combination #4/C GLN 16 NE2     3.796
combination #4/N GLU 30 OE2  combination #4/E ARG 70 CZ      3.802
combination #4/N ILE 69 CD1  combination #4/A ARG 42 NH1     3.805
combination #4/N ALA 41 CB   combination #4/E THR 117 OG1    3.818
combination #4/N ILE 69 CG1  combination #4/A ARG 42 CZ      3.820
combination #4/N GLU 30 OE2  combination #4/E ARG 70 NH1     3.841
combination #4/N SER 38 C    combination #4/C ILE 12 CD1     3.847
combination #4/N SER 38 OG   combination #4/C CYS 14 CB      3.922
combination #4/N SER 43 O    combination #4/C GLN 16 NE2     3.930
combination #4/N SER 59 OG   combination #4/A LYS 46 CG      3.975
combination #4/N SER 59 OG   combination #4/A LYS 46 CB      3.987
combination #4/N ILE 69 CG1  combination #4/A ARG 42 NE      3.994
combination #4/N GLU 30 OE2  combination #4/E ARG 70 NE      4.021
combination #4/N ALA 41 CA   combination #4/E THR 117 OG1    4.021
combination #4/N TYR 37 CZ   combination #4/C LYS 35 NZ      4.039
combination #4/N CYS 44 C    combination #4/C GLN 16 NE2     4.040
combination #4/N SER 59 O    combination #4/A LYS 46 CG      4.085
combination #4/N CYS 44 CB   combination #4/C GLN 16 CD      4.085
combination #4/N GLU 70 OE1  combination #4/A ARG 42 CD      4.097
combination #4/N ARG 40 C    combination #4/E THR 117 OG1    4.100
combination #4/N PHE 63 CE2  combination #4/C GLN 16 OE1     4.103
combination #4/N PHE 63 CZ   combination #4/C GLN 16 OE1     4.120
combination #4/N TYR 23 CE2  combination #4/E ARG 106 CZ     4.121
combination #4/N THR 96 CG2  combination #4/C ARG 19 NH1     4.133
combination #4/N CYS 44 CB   combination #4/C GLN 16 CG      4.147
combination #4/N CYS 39 CB   combination #4/C PRO 59 CG      4.148
combination #4/N SER 43 OG   combination #4/C PRO 59 CB      4.171
combination #4/N TYR 23 CD2  combination #4/E ARG 106 NH1    4.173
combination #4/N TYR 37 CZ   combination #4/C LYS 35 CG      4.175
combination #4/N SER 59 O    combination #4/A LYS 46 NZ      4.182
combination #4/N ILE 69 CG2  combination #4/A ARG 42 NE      4.190
combination #4/N TYR 37 OH   combination #4/C LYS 35 CB      4.190
combination #4/N SER 43 O    combination #4/C GLN 16 CD      4.191
combination #4/N ASP 26 OD1  combination #4/E ARG 106 CZ     4.192
combination #4/N PHE 63 CE2  combination #4/C GLN 16 NE2     4.196
combination #4/N GLN 58 CB   combination #4/A ARG 42 NH1     4.208
combination #4/N GLU 30 OE2  combination #4/E ARG 70 NH2     4.209
combination #4/N SER 38 CB   combination #4/C ILE 12 O       4.235
combination #4/N TYR 23 OH   combination #4/E ARG 106 NH1    4.249
combination #4/N SER 59 CA   combination #4/A LYS 46 CG      4.265
combination #4/N GLY 61 O    combination #4/A LYS 46 CE      4.269
combination #4/N GLN 58 O    combination #4/A LYS 46 CE      4.274
combination #4/N TYR 23 CZ   combination #4/E ARG 106 NH1    4.275
combination #4/N SER 38 CB   combination #4/C CYS 14 CA      4.277
combination #4/N TYR 23 CE2  combination #4/E ARG 106 NH2    4.281
combination #4/N ASP 26 CG   combination #4/E ARG 106 NH2    4.311
combination #4/N SER 43 O    combination #4/C GLN 16 CG      4.316
combination #4/N PHE 63 CE2  combination #4/C GLN 16 CD      4.327
combination #4/N CYS 39 CB   combination #4/C PRO 59 CB      4.328
combination #4/N CYS 44 CA   combination #4/C GLN 16 CD      4.366
combination #4/N GLY 61 C    combination #4/A LYS 46 NZ      4.370
combination #4/N SER 38 O    combination #4/C ILE 12 CB      4.393
combination #4/N ILE 69 CB   combination #4/A ARG 42 NE      4.406
combination #4/N ALA 41 N    combination #4/E THR 117 OG1    4.411
combination #4/N ASP 26 O    combination #4/E ARG 70 NH2     4.425
combination #4/N TYR 37 CZ   combination #4/C LYS 35 CB      4.438
combination #4/N ASP 26 OD1  combination #4/E ARG 106 NH1    4.440
combination #4/N GLU 70 OE1  combination #4/A ARG 42 NE      4.443
combination #4/N TYR 37 CZ   combination #4/C LYS 35 CD      4.447
combination #4/N ARG 40 O    combination #4/E THR 117 CB     4.448
combination #4/N CYS 39 C    combination #4/C ILE 12 CD1     4.449
combination #4/N GLN 58 C    combination #4/A ARG 42 NH1     4.456
combination #4/N SER 38 O    combination #4/C ILE 12 CG1     4.458
combination #4/N ALA 41 CB   combination #4/E VAL 115 CG2    4.473
combination #4/N SER 59 CA   combination #4/A LYS 46 CE      4.493
combination #4/N SER 59 C    combination #4/A LYS 46 CE      4.500

85 distances

hide #!1 models

contacts sel restrict #4/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

26 contacts
           atom1                        atom2              overlap  distance
combination #4/C ILE 12 CD1  combination #4/N CYS 39 CA     0.441    3.319
combination #4/C GLN 16 NE2  combination #4/N CYS 44 CB     0.387    3.133
combination #4/C LYS 35 NZ   combination #4/E ASP 94 CB     0.219    3.301
combination #4/N CYS 44 CA   combination #4/C GLN 16 NE2    0.165    3.355
combination #4/C LYS 35 CE   combination #4/E ASP 94 OD1    0.131    3.169
combination #4/C LYS 35 NZ   combination #4/E ASP 94 CG     0.093    3.427
combination #4/N TYR 23 CE2  combination #4/E ARG 106 NH1   0.021    3.379
combination #4/N TYR 37 OH   combination #4/C LYS 35 NZ     0.004    2.696
combination #4/N ILE 69 CG1  combination #4/A ARG 42 NH1    -0.006    3.526
combination #4/C ILE 12 CD1  combination #4/N CYS 39 CB     -0.028    3.788
combination #4/C LYS 35 CE   combination #4/E ASP 94 CB     -0.074    3.834
combination #4/N TYR 37 OH   combination #4/C LYS 35 CG     -0.133    3.473
combination #4/C LYS 35 NZ   combination #4/E ASP 94 OD1    -0.157    2.817
combination #4/C LYS 35 CE   combination #4/E ASP 94 CG     -0.182    3.942
combination #4/C ILE 12 CD1  combination #4/N CYS 39 N      -0.195    3.715
combination #4/N TYR 37 OH   combination #4/C LYS 35 CD     -0.245    3.585
combination #4/C ARG 19 NH1  combination #4/D GLU 176 CG    -0.271    3.791
combination #4/A ARG 42 NH1  combination #4/N ILE 69 CD1    -0.285    3.805
combination #4/N TYR 37 OH   combination #4/C LYS 35 CE     -0.310    3.650
combination #4/C LYS 35 CE   combination #4/E THR 99 CG2    -0.325    4.085
combination #4/N ILE 69 CG1  combination #4/A ARG 42 CZ     -0.330    3.820
combination #4/C ILE 12 CG1  combination #4/C SF4 3003 S4   -0.332    3.982
combination #4/C ARG 19 NH1  combination #4/D GLU 176 CB    -0.341    3.861
combination #4/N SER 38 C    combination #4/C ILE 12 CD1    -0.357    3.847
combination #4/N CYS 44 CB   combination #4/C GLN 16 CG     -0.387    4.147
combination #4/N CYS 39 CB   combination #4/C PRO 59 CG     -0.388    4.148

26 contacts

ui tool show H-Bonds

select #4/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hbonds sel restrict #4/A-E interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	4 combination

5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
combination #4/A ARG 42 NH1   combination #4/N GLN 58 O    no hydrogen  3.483  N/A
combination #4/A LYS 46 NZ    combination #4/N GLY 61 O    no hydrogen  3.235  N/A
combination #4/C LYS 35 NZ    combination #4/N TYR 37 OH   no hydrogen  2.696  N/A
combination #4/E ARG 106 NH2  combination #4/N ASP 26 OD1  no hydrogen  3.124  N/A
combination #4/E THR 117 OG1  combination #4/N ARG 40 O    no hydrogen  3.442  N/A

5 hydrogen bonds found

select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117

91 atoms, 82 bonds, 9 pseudobonds, 10 residues, 3 models selected

show sel atoms

hide #3 models

hide #4.3 models

select #4#2b&protein

Expected an objects specifier or a keyword

select #4#2 &protein

12712 atoms, 13032 bonds, 72 pseudobonds, 1602 residues, 8 models selected

style sel & #!4 stick

Changed 6356 atom styles

color sel & #!4 byhetero

select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117

91 atoms, 82 bonds, 9 pseudobonds, 10 residues, 3 models selected

show #!1 models

select #1:41-46

60 atoms, 59 bonds, 6 residues, 1 model selected

color sel lime

color sel byhetero

hide #!2.1 models

show #!2.1 models

hide #!2.1 models

show #!2.1 models

show #4.3 models

hide #!4 models

hide #!2.1 models

select #1:HOH

94 atoms, 94 residues, 1 model selected

hide sel atoms

hide #2.2.4 models

show #!4 models

hide #!4 models

select #1:48-51

52 atoms, 52 bonds, 4 residues, 1 model selected

color sel lime

color sel byhetero

select #1:41-43

27 atoms, 26 bonds, 3 residues, 1 model selected

color sel medium blue

color sel byhetero

select #1:9-10

26 atoms, 25 bonds, 2 residues, 1 model selected

color sel lime

color sel byhetero

show #!4 models

hide #!4 models

select #1:15-17

39 atoms, 39 bonds, 3 residues, 1 model selected

color sel lime

color sel byhetero

show #!4 models

select #1:23-31

92 atoms, 92 bonds, 9 residues, 1 model selected

color sel lime

color sel byhetero

hide #!4 models

select #2/C:3003 @<12 &#1:61

6 atoms, 7 bonds, 1 residue, 1 model selected

select #2/C:3003 @<10 &#1:61

2 atoms, 1 bond, 1 residue, 1 model selected

select #2/C:3003 @<9 &#1:61

Nothing selected

select #2/C:3003 @<9.5 &#1:61

1 atom, 1 residue, 1 model selected

select #1:61@S3

1 atom, 1 residue, 1 model selected

select #1:61@S3 @<9.5 &#2/C:3003

1 atom, 1 residue, 1 model selected

select #1:61@S3|#2/C:3003@FE1

2 atoms, 2 residues, 2 models selected

ui tool show Distances

distance #2.2/C:3003@FE1 #1/A:61@S3

Distance between 6yez 2 #2.2/C SF4 3003 FE1 and 2fdn #1/A SF4 61 S3: 9.093Å

help help:user

select @@color="lime"

93 atoms, 72 bonds, 21 residues, 1 model selected

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"

select #2

6384 atoms, 6556 bonds, 69 pseudobonds, 805 residues, 7 models selected

select #2/E

528 atoms, 540 bonds, 66 residues, 1 model selected

style sel stick

Changed 528 atom styles

color sel byhetero

ui tool show "Show Sequence Viewer"

sequence chain #1/A

Alignment identifier is 1/A

select @@color="lime"

93 atoms, 72 bonds, 21 residues, 1 model selected

select #1:1-8,11-14,18-22,32-43,47,52-55

410 atoms, 407 bonds, 34 residues, 1 model selected

hide #!2 models

open 6yez

6yez title:
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]

Chain information for 6yez #6
Chain	Description	UniProt
1	Lhca1
2	Chlorophyll a-b binding protein, chloroplastic	Q41038_PEA 58-265
3	Chlorophyll a-b binding protein 3, chloroplastic	CB23_PEA 55-275
4	Chlorophyll a-b binding protein P4, chloroplastic	CB24_PEA 52-249
A	Photosystem I P700 chlorophyll a apoprotein A1	A0A0F6NFW5_PEA 16-758
B	Photosystem I P700 chlorophyll a apoprotein A2	A0A0F6NGI2_PEA 2-734
C	Photosystem I iron-sulfur center	PSAC_PEA 2-81
D	PsaD
E	PsaE
F	PsaF
G	PsaG
H	PsaH
I	Photosystem I reaction center subunit VIII	PSAI_PEA 2-32
J	PsaJ
K	Photosystem I reaction center subunit X psaK	E1C9L3_PEA 46-126
L	PsaL
N	Ferredoxin-1, chloroplastic	FER1_PEA 1-97
P	Plastocyanin, chloroplastic	PLAS_PEA 1-99

Non-standard residues in 6yez #6
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
C7Z — (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol ((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)

select add #6

39627 atoms, 41140 bonds, 678 pseudobonds, 3718 residues, 3 models selected

select add #1

39979 atoms, 41414 bonds, 686 pseudobonds, 3835 residues, 4 models selected

select subtract #1

39217 atoms, 40733 bonds, 678 pseudobonds, 3684 residues, 2 models selected

hide sel atoms

show sel cartoons

select #6/F-Z

8235 atoms, 8462 bonds, 68 pseudobonds, 894 residues, 2 models selected

hide sel cartoons

select #6/F-Z/1-4

18908 atoms, 19592 bonds, 309 pseudobonds, 1801 residues, 2 models selected

hide sel cartoons

log metadata #6

Metadata for 6yez #6
Title	Plant PSI-ferredoxin-plastocyanin supercomplex
Citation	Caspy, I., Borovikova-Sheinker, A., Klaiman, D., Shkolnisky, Y., Nelson, N. (2020). The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. Nat.Plants, 6, 1300-1305. PMID: 33020607. DOI: 10.1038/s41477-020-00779-9
Non-standard residues	3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
	BCR — β-carotene
	C7Z — (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
	CA — calcium ion
	CHL — chlorophyll B
	CL0 — chlorophyll A isomer
	CLA — chlorophyll A
	CU — copper (II) ion
	DGD — digalactosyl diacyl glycerol (DGDG)
	FES — FE2/S2 (inorganic) cluster
	LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
	LMG — 1,2-distearoyl-monogalactosyl-diglyceride
	LMT — dodecyl-β-D-maltoside
	LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol ((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
	PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
	SF4 — iron/sulfur cluster
	XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)
Sources (natural)	Pisum sativum (garden pea)
Sources (natural)	Pisum sativum (pea)
CryoEM Map	EMDB 10798 — open map
Experimental method	Electron microscopy
Resolution	2.7Å

select #6/F-Z/1-4

18908 atoms, 19592 bonds, 309 pseudobonds, 1801 residues, 2 models selected

show sel cartoons

hide sel cartoons

show sel cartoons

hide sel cartoons

show sel cartoons

hide sel cartoons

show sel cartoons

show sel atoms

delete atoms (#!6 & sel)

delete bonds (#!6 & sel)

combine #1#6

Remapping chain ID 'A' in 6yez #6 to 'F'

hide #!6 models

hide #!1 models

hide #!7 models

show #!7 models

close #7

show #!6 models

show #!1 models

select #6/N

Nothing selected

ui tool show "Change Chain IDs"

select #1

762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected

ui tool show "Change Chain IDs"

changechains sel M

Chain IDs of 151 residues changed

combine #1#6

hide #!6 models

hide #!1 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/Bfdx_PSI_toDiffusion.pdb" models #7

combine #7/A:700

close #8

select #7/A:700

14 atoms, 15 bonds, 1 residue, 1 model selected

select #7/A:740

8 atoms, 7 bonds, 1 residue, 1 model selected

select #7/A:759

Nothing selected

select #7/A:758

5 atoms, 4 bonds, 1 residue, 1 model selected

select #7/A:758/B:2

10 atoms, 8 bonds, 2 residues, 1 model selected

hide #!7 models

show #!2 models

select #2/A:758/B:724

Nothing selected

select #2/A:758/B:707

8 atoms, 7 bonds, 1 residue, 1 model selected

select #2/B:696/C:2

15 atoms, 13 bonds, 2 residues, 1 model selected

select #2/B:696@C/C:2@N

2 atoms, 2 residues, 1 model selected

select #2/B:696@C/C:2@N

2 atoms, 2 residues, 1 model selected

distance #2.2/B:696@C #2.2/C:2@N

Distance between 6yez 2 #2.2/B LYS 696 C and /C SER 2 N: 16.567Å

select #2/D:59@N/C:81@C

1 atom, 1 residue, 1 model selected

select #2/D:69@N/C:81@C

2 atoms, 2 residues, 1 model selected

distance #2.2/C:81@C #2.2/D:69@N

Distance between 6yez 2 #2.2/C TYR 81 C and /D GLY 69 N: 36.658Å

select #2/E:64@N/D:211@C

2 atoms, 2 residues, 1 model selected

distance #2.2/E:64@N #2.2/D:211@C

Distance between 6yez 2 #2.2/E PRO 64 N and /D LEU 211 C: 36.932Å

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb"

Chain information for PSI_stromal_ridge_0.pdb #8
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #8 to #2.2 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6yez 2, chain A (#2.2) with PSI_stromal_ridge_0.pdb, chain A (#8), sequence alignment score = 924.3
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A, PSI_stromal_ridge_0.pdb #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs: 0.259)

sequence header consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 1

select #8/A:59

4 atoms, 3 bonds, 1 residue, 1 model selected

select #8/A:59-62

16 atoms, 15 bonds, 4 residues, 1 model selected

select #8:59-62

16 atoms, 15 bonds, 4 residues, 1 model selected

show sel atoms

hide sel cartoons

select #8:58-63

24 atoms, 23 bonds, 6 residues, 1 model selected

show sel atoms

hide sel cartoons

select #2/A:192

9 atoms, 8 bonds, 1 residue, 1 model selected

show sel atoms

style sel stick

Changed 9 atom styles

color sel byhetero

hide sel cartoons

ui tool show "Build Structure"

combine #8

Associated copy of PSI_stromal_ridge_0.pdb chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A, PSI_stromal_ridge_0.pdb #8/A, copy of PSI_stromal_ridge_0.pdb #9/A

help help:user

ui tool show "Show Sequence Viewer"

sequence chain #9/A

Alignment identifier is 9/A

select #9 sequence GGGG

676 atoms, 663 bonds, 169 residues, 1 model selected

select #9:59-62,73-76,117-120,147-150,185-192,228-257,301-304,320-323,365-368,398-401,443-470,551-586,729-763

676 atoms, 663 bonds, 169 residues, 1 model selected

color sel cyan

hide #8 models

hide #!2 models

show #!2 models

select add #2.2

6332 atoms, 6479 bonds, 68 pseudobonds, 876 residues, 6 models selected

style sel stick

Changed 6332 atom styles

select add #2

7060 atoms, 7219 bonds, 72 pseudobonds, 974 residues, 9 models selected

select subtract #2

676 atoms, 663 bonds, 169 residues, 1 model selected

hide #!2.2 models

show #!2.1 models

help help:user

split #9 atoms :59-62 atoms :73-76 atoms :117-120 atoms :147-150 atoms :185-192 atoms :228-257 atoms :301-304 atoms :320-323 atoms :365-368 atoms :398-401 atoms :443-470 atoms :551-586 atoms :729-763

Split copy of PSI_stromal_ridge_0.pdb (#9) into 14 models

Chain information for copy of PSI_stromal_ridge_0.pdb 1 #9.1
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 2 #9.2
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 3 #9.3
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 4 #9.4
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 5 #9.5
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 6 #9.6
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 7 #9.7
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 8 #9.8
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 9 #9.9
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 10 #9.10
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 11 #9.11
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 12 #9.12
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 13 #9.13
Chain	Description
A	No description available

Chain information for copy of PSI_stromal_ridge_0.pdb 14 #9.14
Chain	Description
A	No description available

Associated copy of PSI_stromal_ridge_0.pdb 6 (9.6) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 11 (9.11) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 12 (9.12) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 13 (9.13) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 14 (9.14) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A, PSI_stromal_ridge_0.pdb #8/A, copy of PSI_stromal_ridge_0.pdb 6 #9.6/A, copy of PSI_stromal_ridge_0.pdb 11 #9.11/A, copy of PSI_stromal_ridge_0.pdb 12 #9.12/A, copy of PSI_stromal_ridge_0.pdb 13 #9.13/A, copy of PSI_stromal_ridge_0.pdb 14 #9.14/A

hide #9.14 models

show #!2.2 models

3316 atoms, 3289 bonds, 829 residues, 15 models selected

select subtract #9.14

676 atoms, 663 bonds, 169 residues, 14 models selected

show sel atoms

hide sel cartoons

color sel byhetero

3316 atoms, 3289 bonds, 829 residues, 15 models selected

select subtract #9

Nothing selected

hide #9.13 models

hide #9.12 models

hide #9.11 models

hide #9.10 models

hide #9.9 models

hide #9.8 models

hide #9.7 models

hide #9.6 models

hide #9.5 models

hide #9.4 models

hide #9.3 models

hide #9.2 models

ui tool show "Add Hydrogens"

ui tool show "Build Structure"

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

——— End of log from Sat May 18 14:49:43 2024 ———

opened ChimeraX session

select #9.1:58@C:59@N

1 atom, 1 residue, 1 model selected

show #9.14 models

~bond sel

select #2/A:73@C#9.1:59@N

2 atoms, 2 residues, 2 models selected

hide sel cartoons

show sel atoms

build join peptide sel length 1.33 omega 180 phi -120 move small

No chain-terminal carbons in atoms

~bond sel

select #2.2/A:73@C#9.1:59@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move small

No chain-terminal carbons in atoms

hide #9.14 models

show #9.14 models

hide #9.14 models

show #9.14 models

hide #9.14 models

show #9.14 models

hide #9.14 models

show #9.14 models

hide #9.14 models

split #2.2 atoms /A:1-73

Split 6yez 2 (#2.2) into 2 models

Chain information for 6yez 2 1 #2.2.1
Chain	Description
A	No description available

Chain information for 6yez 2 2 #2.2.2
Chain	Description
A	No description available
B	No description available
C	No description available
D	No description available
E	No description available

Associated 6yez 2 1 (2.2.1) chain A to 6yez 2, chain A with 0 mismatches
Associated 6yez 2 2 (2.2.2) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 2 (2.2.2) chain D to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 2 (2.2.2) chain C to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 2 (2.2.2) chain E to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches

hide #!2.2.2 models

select #2.2.1/A:73

9 atoms, 8 bonds, 1 residue, 1 model selected

show sel atoms

color sel byhetero

select #2.2.1/A:73@C#9.1:59@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move small

show #8 models

help help:user

align #2.2.1/A:132-135 toAtoms #8:59-63 matchAtomNames true move residues

Pairing dropped 0 atoms and 4 reference atoms
RMSD between 16 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

hide #2.2.1 models

hide #8 models

show #!2.2.2 models

show #2.2.1 models

align #2.2.2/A:191

Missing required "to_atoms" argument

select #2.2.2/A:191

7 atoms, 7 bonds, 1 residue, 1 model selected

show sel atoms

hide sel cartoons

color sel byhetero

select #2.2.2/A:191@N#2.2.1/A:135@C

2 atoms, 2 residues, 2 models selected

ui tool show "Build Structure"

build join peptide sel length 1.33 omega 180 phi -120 move N

show #!4 models

hide #!4 models

select #2.2.1/A:191

7 atoms, 7 bonds, 1 residue, 1 model selected

hide #!2 models

show #!4 models

select #4/A:191-*

Expected an objects specifier or a keyword

select #4/A:191-707/B-E

5003 atoms, 5138 bonds, 26 pseudobonds, 626 residues, 4 models selected

select #2.2.1/A:191-707/B-E

5003 atoms, 5138 bonds, 60 pseudobonds, 626 residues, 4 models selected

hide #!2.1 models

show #!2.1 models

select #2.2.1/A:191-707/B-E to #4/A:191-707/B-E matchA t matchN t move res

Expected a keyword

align #2.2.1/A:191-707/B-E toAtoms #4/A:191-707/B-E matchAtomNames true matchNumbering true move residues

RMSD between 5003 atom pairs is 0.000 angstroms

align #2.2.1/A:708-729,3001 toAtoms #4/A:708-729,3001 matchAtomNames true matchNumbering true move residues

RMSD between 179 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

hide #!2.2 models

show #!2.2 models

hide #!2.2.1 models

show #!2.2.1 models

hide #!2.2.1 models

show #!2.2.1 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

select #2.2.1/A:315-354,417-442,562-595,695-729/B:2-44,162-176,291-331,392-420,535-575,665-696/C/D/E

5004 atoms, 5140 bonds, 59 pseudobonds, 627 residues, 4 models selected

split #2.2.1 atoms /A:315-354 atoms /A:417-442 atoms /A:562-595 atoms /A:695-729 atoms /B:2-44 atoms /B:162-176 atoms /B:291-331 atoms /B:392-420 atoms /B:535-575 atoms /B:665-696 atoms /C atoms /D atoms /E

Split 6yez 2 1 (#2.2.1) into 14 models

Chain information for 6yez 2 1 1 #2.2.1.1
Chain	Description
A	No description available

Chain information for 6yez 2 1 2 #2.2.1.2
Chain	Description
A	No description available

Chain information for 6yez 2 1 3 #2.2.1.3
Chain	Description
A	No description available

Chain information for 6yez 2 1 4 #2.2.1.4
Chain	Description
A	No description available

Chain information for 6yez 2 1 5 #2.2.1.5
Chain	Description
B	No description available

Chain information for 6yez 2 1 6 #2.2.1.6
Chain	Description
B	No description available

Chain information for 6yez 2 1 7 #2.2.1.7
Chain	Description
B	No description available

Chain information for 6yez 2 1 8 #2.2.1.8
Chain	Description
B	No description available

Chain information for 6yez 2 1 9 #2.2.1.9
Chain	Description
B	No description available

Chain information for 6yez 2 1 10 #2.2.1.10
Chain	Description
B	No description available

Chain information for 6yez 2 1 11 #2.2.1.11
Chain	Description
C	No description available

Chain information for 6yez 2 1 12 #2.2.1.12
Chain	Description
D	No description available

Chain information for 6yez 2 1 13 #2.2.1.13
Chain	Description
E	No description available

Chain information for 6yez 2 1 14 #2.2.1.14
Chain	Description
A	No description available
B	No description available

Associated 6yez 2 1 1 (2.2.1.1) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 2 (2.2.1.2) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 3 (2.2.1.3) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 4 (2.2.1.4) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 5 (2.2.1.5) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 6 (2.2.1.6) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 7 (2.2.1.7) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 8 (2.2.1.8) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 9 (2.2.1.9) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 11 (2.2.1.11) chain C to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 12 (2.2.1.12) chain D to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 13 (2.2.1.13) chain E to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 14 (2.2.1.14) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated 6yez 2 1 14 (2.2.1.14) chain B to 6yez 2, chain A with 1 mismatch

hide #2.2.1.14 models

show #2.2.1.14 models

hide #2.2.1.14 models

show #2.2.1.14 models

hide #2.2.1.13 models

show #2.2.1.13 models

hide #2.2.1.1 models

show #2.2.1.1 models

hide #2.2.1.1 models

show #2.2.1.1 models

hide #!2.2.1 models

show #!2.2.1 models

hide #2.2.1.1 models

show #2.2.1.1 models

show #9.2 models

select #2.2/A:200@C#9.2:73@N

2 atoms, 2 residues, 2 models selected

show sel atoms

hide sel cartoons

show sel cartoons

hide sel cartoons

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:273-276 toAtoms #8:73-76 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

show #8 models

hide #8 models

select #2.2/A:276@C:315@N

2 atoms, 2 residues, 2 models selected

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:315-354 toAtoms #4/A:315-354 matchAtomNames true matchNumbering true move residues

RMSD between 322 atom pairs is 0.000 angstroms

select #2.2/A:276-315

14 atoms, 14 bonds, 2 residues, 1 model selected

show sel cartoons

select #2.2/A:72-315

149 atoms, 153 bonds, 21 residues, 1 model selected

show sel cartoons

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #9.3 models

select #2.2/A:354@C#9.3:117@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

show #8 models

align #2.2.1/A:117-120 toAtoms #8:117-120 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

hide #8 models

select up

14 atoms, 15 bonds, 1 residue, 1 model selected

select down

1 atom, 1 residue, 1 model selected

select #2.2/A:120@C#2.2:417@N

3 atoms, 3 residues, 3 models selected

hide #2.2.1.8 models

show #2.2.1.8 models

hide #2.2.1.8 models

show #2.2.1.8 models

hide #2.2.1.2 models

show #2.2.1.2 models

select #2.2/A:120@C#2.2:417@N

3 atoms, 3 residues, 3 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:417-442 toAtoms #4/A:417-442 matchAtomNames true matchNumbering true move residues

RMSD between 228 atom pairs is 0.000 angstroms

select #2.2.1/A:417-442

228 atoms, 232 bonds, 26 residues, 1 model selected

show sel cartoons

[Repeated 1 time(s)]

select #2.2.1/A:72-442

705 atoms, 725 bonds, 90 residues, 1 model selected

show sel cartoons

show #9.4 models

select #2.2/A:442@C#9.4:147@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:147-150 toAtoms #8:147-150 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

select #2.2/A:150@C#2.2:562@N

3 atoms, 3 residues, 3 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:562-595 toAtoms #4/A:562-595 matchAtomNames true matchNumbering true move residues

RMSD between 257 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #8 models

hide #8 models

show #8 models

hide #8 models

show #9.5 models

select #2.2/A:595@C#9.5:185@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:780-787 toAtoms #8:185-192 matchAtomNames true move residues

RMSD between 32 atom pairs is 0.000 angstroms

select #2.2/A:787@C#2.2:695@N

3 atoms, 3 residues, 3 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:695-729 toAtoms #4/A:695-729 matchAtomNames true matchNumbering true move residues

RMSD between 279 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #8 models

hide #2.2.1.14 models

show #2.2.1.14 models

hide #2.2.1.14 models

show #2.2.1.14 models

select #2.2/A

1753 atoms, 1810 bonds, 228 residues, 1 model selected

show sel cartoons

hide #8 models

show #9.6 models

select #2.2/A:729@C#9.6:228@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:228-257 toAtoms #8:228-257 matchAtomNames true move residues

RMSD between 120 atom pairs is 0.000 angstroms

select #2.2/A:257@C#2.2/B:2@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true matchNumbering true move residues

Pairing dropped 356 atoms and 356 reference atoms
No atoms paired for alignment

show #!4 models

align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true move residues

RMSD between 356 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #9.7 models

hide #9.7 models

show #9.7 models

select #2.2/A:831@C#9.7:301@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:301-304 toAtoms #8:301-304 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

hide #!4 models

select #2.2/A:304@C#2.2/B:162@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:162-176 toAtoms #4/B:162-176 matchAtomNames true move residues

RMSD between 124 atom pairs is 0.000 angstroms

show #9.8 models

select #2.2/A:176@C#9.8:320@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:1151-1154 toAtoms #8:320-323 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

select #2.2/A:1154@C#2.2/B:291@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:1445-1485 toAtoms #4/B:291-331 matchAtomNames true move residues

RMSD between 324 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #9.9 models

hide #9.9 models

show #9.9 models

select #2.2/A:1485@C#9.9:365@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:365-368 toAtoms #8:365-368 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

select #2.2/A:368@C#2.2/B:392@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:1877-1905 toAtoms #4/B:392-420 matchAtomNames true move residues

RMSD between 242 atom pairs is 0.000 angstroms

show #9.10 models

select #2.2/A:1905@C#9.10:398@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:398-401 toAtoms #8:398-401 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

select #2.2/A:401@C#2.2/B:535@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:2440-2480 toAtoms #4/B:535-575 matchAtomNames true move residues

RMSD between 299 atom pairs is 0.000 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #9.11 models

select #2.2/A:2480@C#9.11:443@N

2 atoms, 2 residues, 2 models selected

select #2.2/A:2480@C#9.11:443@N

2 atoms, 2 residues, 2 models selected

show #8 models

select #2.2/A

3282 atoms, 3377 bonds, 443 residues, 1 model selected

show sel cartoons

hide #2.2.1.14 models

show #2.2.1.14 models

hide #2.2.1.14 models

show #2.2.1.14 models

hide #2.2.1.10 models

show #2.2.1.10 models

hide #2.2.1.14 models

show #2.2.1.14 models

select #2.2/A:2480@C#9.11:443@N

2 atoms, 2 residues, 2 models selected

hide #8 models

show #8 models

hide #8 models

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:443-470 toAtoms #8:443-470 matchAtomNames true move residues

RMSD between 112 atom pairs is 0.000 angstroms

show #9.12 models

hide #9.12 models

show #8 models

hide #8 models

select #2.2/A:470@C#2.2/C:2@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:2482-2561 toAtoms #4/C:2-81 matchAtomNames true move residues

RMSD between 612 atom pairs is 0.000 angstroms

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

align #2.2.1/A:3002-3003 toAtoms #4/C:3002-3003 matchAtomNames true move residues

RMSD between 16 atom pairs is 0.000 angstroms

hide #!4 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

show #9.12 models

select #2.2/A:2561@C#9.11:551@N

1 atom, 1 residue, 1 model selected

build join peptide sel length 1.33 omega 180 phi -120 move N

No nitrogens in specified atoms

select #2.2/A:2561@C#9.12:551@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

show #8 models

hide #8 models

show #8 models

align #2.2.1/A:3112-3147 toAtoms #8:551-586 matchAtomNames true move residues

RMSD between 144 atom pairs is 0.000 angstroms

hide #8 models

show #!4 models

hide #2.2.1.10 models

hide #2.2.1.12 models

show #2.2.1.12 models

hide #2.2.1.12 models

show #2.2.1.12 models

hide #2.2.1.12 models

show #2.2.1.12 models

hide #2.2.1.12 models

hide #2.2.1.13 models

hide #!2.2.1.14 models

show #!2.2.1.14 models

show #9.13 models

hide #9.13 models

show #9.13 models

hide #9.13 models

show #9.13 models

hide #9.13 models

hide #!4 models

show #2.2.1.13 models

hide #2.2.1.13 models

show #2.2.1.12 models

select #2/D:69

4 atoms, 3 bonds, 1 residue, 1 model selected

hide sel cartoons

show sel atoms

color sel byhetero

select #2.2/A:3147@C#2.2/D:69@N

2 atoms, 2 residues, 2 models selected

build join peptide sel length 1.33 omega 180 phi -120 move N

align #2.2.1/A:3216-3358 toAtoms #4/D:69-211 matchAtomNames true move residues

RMSD between 1132 atom pairs is 0.000 angstroms

show #!4 models

hide #!4 models

show #2.2.1.10 models

hide #2.2.1.10 models

show #2.2.1.10 models

show #9.13 models

show #!4 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs"

——— End of log from Sat May 18 17:13:54 2024 ———

opened ChimeraX session

close #2.2

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

close #6

close #8#9

close #7

close #3

close #5

hide #!2.1 models

show #!2.1 models

close #2

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs"

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb" format pdb

Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb
warnings	Ignored bad PDB record found on line 34701 SEQRES * A 830 Ignored bad PDB record found on line 34702 SEQRES * A 830 Ignored bad PDB record found on line 34703 SEQRES * A 830 Ignored bad PDB record found on line 34704 SEQRES * A 830 Ignored bad PDB record found on line 34705 SEQRES *** A 830 92885266 messages similar to the above omitted

Chain information for SingleChainStromalRidge_PetF_Fdn.pdb #2
Chain	Description
A	No description available
M	No description available
N	No description available

help help:user/tools/modelpanel.html

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb" models #2

hide #!4 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide sel cartoons

show sel cartoons

select #2

7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected

ui tool show "Color Actions"

color sel bychain

select #2:FES,SF4

44 atoms, 64 bonds, 6 residues, 1 model selected

color sel byhetero

select #2

7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected

color sel byhetero

show sel atoms

[Repeated 1 time(s)]

hide sel atoms

select #2:FES,SF4,CYS

238 atoms, 231 bonds, 19 pseudobonds, 33 residues, 2 models selected

show sel atoms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs"

——— End of log from Sat May 18 22:45:24 2024 ———

opened ChimeraX session

hide #!2 models

show #!4 models

close #2

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs"

ui tool show "Show Sequence Viewer"

Alignment identifier is 4/A

select #4/A:729

9 atoms, 8 bonds, 1 residue, 1 model selected

select #4/A:729

9 atoms, 8 bonds, 1 residue, 1 model selected

rename #4 id 2

select #2/A:16-73,191-200,315-354,417-442,562-595,695-729

1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs"

select #2/A:16-73

474 atoms, 490 bonds, 58 residues, 1 model selected

ui tool show "Renumber Residues"

renumber #2/A:16-73 start 1

58 residues renumbered

select #2/A:191

7 atoms, 7 bonds, 1 residue, 1 model selected

select #2/A:191

7 atoms, 7 bonds, 1 residue, 1 model selected

select #2/A:191-200

89 atoms, 92 bonds, 10 residues, 1 model selected

renumber #2/A:191-200 start 63

10 residues renumbered

select #2/A:315-354

322 atoms, 333 bonds, 40 residues, 1 model selected

renumber #2/A:315-354 start 77

40 residues renumbered

select #2/A:417-442

228 atoms, 232 bonds, 26 residues, 1 model selected

renumber #2/A:417-442 start 121

26 residues renumbered

select #2/A:562-595

257 atoms, 264 bonds, 34 residues, 1 model selected

renumber #2/A:562-595 start 151

34 residues renumbered

select #2/A:695-729

279 atoms, 286 bonds, 35 residues, 1 model selected

renumber #2/A:695-729 start 193

35 residues renumbered

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs"

ui tool show "Show Sequence Viewer"

sequence chain #2/B

Alignment identifier is 2/B

select #2/B:2-44,162-176,291-331,392-420,535-575,665-696/A:227

1639 atoms, 1681 bonds, 5 pseudobonds, 202 residues, 2 models selected

select #2/B:2-44/A:227

365 atoms, 374 bonds, 44 residues, 1 model selected

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb"

Chain information for PSI_stromal_ridge_0.pdb #3
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #3 to #2

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker combination, chain A (#2) with PSI_stromal_ridge_0.pdb, chain A (#3), sequence alignment score = 924.3
RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs: 0.259)

select #2/B:2-44/A:227

365 atoms, 374 bonds, 44 residues, 1 model selected

hide #3 models

show #3 models

select #2/B:2-44

356 atoms, 366 bonds, 43 residues, 1 model selected

renumber #2/B:2-44 start 258

Proposed renumbering conflicts with existing residue combination #2/B TYR 291

select #2/B:2-44,162-176,291-331,392-420,535-575,665-696

1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected

select #2/B:2-44,162-176,291-331,392-420,535-575,665-696

1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected

renumber #2/B:2-696 start 1002

201 residues renumbered

select #2/B:697

7 atoms, 7 bonds, 1 residue, 1 model selected

select #2/B:697-707

81 atoms, 81 bonds, 11 residues, 1 model selected

renumber #2/B:697-707 start 1697

11 residues renumbered

select #3 sequence GGGG

676 atoms, 663 bonds, 169 residues, 1 model selected

color sel cyan

hide #3 models

show #3 models

hide #3 models

select #2/B:1002-1044

356 atoms, 366 bonds, 43 residues, 1 model selected

show #3 models

renumber #2/B:1002-1044 start 258

43 residues renumbered

select #2/B:1162-1176

124 atoms, 127 bonds, 15 residues, 1 model selected

select #2/B:300

9 atoms, 8 bonds, 1 residue, 1 model selected

select #2/B:300-1162

18 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1162-1176

124 atoms, 127 bonds, 15 residues, 1 model selected

renumber #2/B:1162-1176 start 305

15 residues renumbered

select #2/B:319

8 atoms, 7 bonds, 1 residue, 1 model selected

select #2/B:319-1291

20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1291-1331

324 atoms, 333 bonds, 41 residues, 1 model selected

hide #3 models

hide #!2 models

show #!2 models

select #2/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide sel atoms

hide sel cartoons

show #!1 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_0.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_1.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_2.pdb"

Chain information for PSI_fdn_0.pdb #4
Chain	Description
A	No description available

Chain information for PSI_fdn_1.pdb #5
Chain	Description
A	No description available

Chain information for PSI_fdn_2.pdb #6
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #4-6 to #1

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 2fdn, chain M (#1) with PSI_fdn_0.pdb, chain A (#4), sequence alignment score = 139.6
RMSD between 46 pruned atom pairs is 0.501 angstroms; (across all 53 pairs: 2.902)

Matchmaker 2fdn, chain M (#1) with PSI_fdn_1.pdb, chain A (#5), sequence alignment score = 147.1
RMSD between 47 pruned atom pairs is 0.590 angstroms; (across all 53 pairs: 2.756)

Matchmaker 2fdn, chain M (#1) with PSI_fdn_2.pdb, chain A (#6), sequence alignment score = 135.4
RMSD between 44 pruned atom pairs is 0.540 angstroms; (across all 48 pairs: 2.878)

select #4-6/A

10668 atoms, 10665 bonds, 2667 residues, 3 models selected

select #4-6:1-831

9972 atoms, 9969 bonds, 2493 residues, 3 models selected

hide sel atoms

hide sel cartoons

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target.cxs"

show #3 models

hide #3 models

close #4-6

select #2/B:1291-1331

324 atoms, 333 bonds, 41 residues, 1 model selected

show #3 models

select #2/B:319

8 atoms, 7 bonds, 1 residue, 1 model selected

select #2/B:319-1291

20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1291-1331

324 atoms, 333 bonds, 41 residues, 1 model selected

renumber #2/B:1291-1331 start 305

Proposed renumbering conflicts with existing residue combination #2/B LYS 305

select #2/B:305

9 atoms, 8 bonds, 1 residue, 1 model selected

select #2/B:2-44,162-176,291-331,392-420,535-575,665-696

208 atoms, 211 bonds, 1 pseudobond, 25 residues, 2 models selected

hide #3 models

select #2/B:1291-1331

324 atoms, 333 bonds, 41 residues, 1 model selected

show #3 models

renumber #2/B:1291-1331 start 324

41 residues renumbered

select #2/B:1392-1420

242 atoms, 246 bonds, 29 residues, 1 model selected

select #2/B:364

10 atoms, 10 bonds, 1 residue, 1 model selected

select #2/B:364-1392

18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1392-1420

242 atoms, 246 bonds, 29 residues, 1 model selected

select #2/B:364

10 atoms, 10 bonds, 1 residue, 1 model selected

select #2/B:364-1392

18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1392-1420

242 atoms, 246 bonds, 29 residues, 1 model selected

renumber #2/B:1392-1420 start 369

29 residues renumbered

select #2/B:397

6 atoms, 5 bonds, 1 residue, 1 model selected

select #2/B:397-1535

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1535-1575

299 atoms, 306 bonds, 41 residues, 1 model selected

renumber #2/B:1535-1575 start 402

41 residues renumbered

select #2/B:1665-1696

285 atoms, 295 bonds, 32 residues, 1 model selected

select #2/B:442

5 atoms, 4 bonds, 1 residue, 1 model selected

select #2/B:442-1665

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected

select #2/B:1665-1696

285 atoms, 295 bonds, 32 residues, 1 model selected

select #2/B:1665-170

Nothing selected

show cartoons

select #2/B:1665-1707

366 atoms, 377 bonds, 43 residues, 1 model selected

show sel cartoons

renumber #2/B:1665-1707 start 451

43 residues renumbered

hide #3 models

select #2/B

1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected

select #2/B

1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected

select #2/C

628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected

select #2/C

628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected

select #2/C:2-81

612 atoms, 625 bonds, 80 residues, 1 model selected

show sel cartoons

select #2/C:2

6 atoms, 5 bonds, 1 residue, 1 model selected

show #3 models

renumber #2/C:2 start 471

1 residues renumbered

ui tool show "Show Sequence Viewer"

sequence chain #2/C

Alignment identifier is 2/C

select #2/C:2-81

606 atoms, 619 bonds, 79 residues, 1 model selected

renumber #2/C:3-81 start 472

79 residues renumbered

select #2/D

1132 atoms, 1163 bonds, 143 residues, 1 model selected

select #2/D

1132 atoms, 1163 bonds, 143 residues, 1 model selected

renumber #2/D start 587

143 residues renumbered

select #2/E

528 atoms, 540 bonds, 66 residues, 1 model selected

renumber #2/E start 764

66 residues renumbered

hide #3 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target reunumbered.cxs"

ui tool show "Show Sequence Viewer"

sequence chain #2/D

Alignment identifier is 2/D

ui tool show "Show Sequence Viewer"

sequence chain #2/E

Alignment identifier is 2/E

select #2/D

1132 atoms, 1163 bonds, 143 residues, 1 model selected

select #2/D:701-729

224 atoms, 228 bonds, 29 residues, 1 model selected

hide sel cartoons

select #2/B

1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected

hide sel cartoons

show sel cartoons

[Repeated 1 time(s)]

hide sel cartoons

select #2/A:1-15

119 atoms, 120 bonds, 15 residues, 1 model selected

hide sel cartoons

select #2/A:1-15,63-115

516 atoms, 529 bonds, 1 pseudobond, 64 residues, 2 models selected

select #2/A:1-15,63-146

758 atoms, 777 bonds, 2 pseudobonds, 91 residues, 2 models selected

hide sel cartoons

select #2/A:1-15,63-146/C/D:587-700/E

2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected

ui tool show "Change Chain IDs"

changechains sel A

Cannot reassign chain ID to only part of polymeric chain (combination #2/A)

combine #2

rename #4 "Stromal ridge small"

select #2/A:1-15,63-146/C/D:587-700/E

2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected

hide sel cartoons

[Repeated 1 time(s)]

show sel cartoons

hide #!2 models

select #4/A:1-15,63-146/C/D:587-700/E

2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected

hide sel cartoons

[Repeated 1 time(s)]

show sel cartoons

[Repeated 1 time(s)]

hide sel cartoons

[Repeated 1 time(s)]

show sel cartoons

hide sel cartoons

show sel cartoons

show #!2 models

hide #!4 models

select #2/A:1-15,63-146/C/D:587-700/E

2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected

select #2/A:16-62,147/C/D:587-700/E

2419 atoms, 2492 bonds, 17 pseudobonds, 305 residues, 3 models selected

select #2/A:16-62,147-227/C/D:587-700/E

2955 atoms, 3042 bonds, 18 pseudobonds, 374 residues, 4 models selected

select #2/A:16-62,147-227,3001/C/D:587-700/E

2963 atoms, 3054 bonds, 20 pseudobonds, 375 residues, 4 models selected

select #4/A:1-15,63-146/B/D:701-729

2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected

select #4/A:1-15,63-146/B/D:701-729

2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected

select #4/A:1-15,63-146/B/D:701-729

2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected

show #!4 models

hide #!2 models

select #4/A:1-15,63-146/D:701-729

982 atoms, 1005 bonds, 2 pseudobonds, 120 residues, 2 models selected

hide sel cartoons

select #4/A:1-12,46-146/D:701-729

1065 atoms, 1090 bonds, 3 pseudobonds, 130 residues, 2 models selected

select #4/A:1-12,55-146/D:701-729

994 atoms, 1016 bonds, 3 pseudobonds, 121 residues, 2 models selected

hide sel cartoons

select #4/B

1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected

show sel cartoons

select #4/B &~:425-436

1635 atoms, 1676 bonds, 5 pseudobonds, 200 residues, 2 models selected

hide sel cartoons

select #4/A:16-54,151-227,3001/C/D:587-700/E

2929 atoms, 3020 bonds, 20 pseudobonds, 371 residues, 4 models selected

hide sel cartoons

show sel cartoons

select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E

3005 atoms, 3097 bonds, 22 pseudobonds, 383 residues, 4 models selected

hide sel cartoons

show sel cartoons

surface #4 enclose #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E

coulombic sel

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for Stromal ridge small_A SES surface #4.5: minimum, -23.39, mean -1.01, maximum 11.65
Coulombic values for Stromal ridge small_B SES surface #4.6: minimum, -18.54, mean 0.17, maximum 12.46
Coulombic values for Stromal ridge small_C SES surface #4.7: minimum, -12.54, mean -0.30, maximum 9.66
Coulombic values for Stromal ridge small_D SES surface #4.8: minimum, -11.89, mean 1.48, maximum 14.01
Coulombic values for Stromal ridge small_E SES surface #4.9: minimum, -13.21, mean 1.18, maximum 10.80
To also show corresponding color key, enter the above coulombic command and add key true

close #4.5-9

select add #4.4

3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected

select subtract #4.4

3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected

select add #4.4

3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected

select subtract #4.4

3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected

select add #4.4

3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected

close #4.4

select #4/M

Nothing selected

select #4/N

728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected

hide #!1 models

hide sel cartoons

hide sel atoms

select #4 &@@display

184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected

select #4 &@@~display

184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected

show sel atoms

select #4 &~@@display

6200 atoms, 6338 bonds, 4 pseudobonds, 784 residues, 2 models selected

show sel atoms

hide sel atoms

select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E

3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected

hide sel cartoons

hide sel atoms

show sel cartoons

show sel atoms

select #4

6384 atoms, 6556 bonds, 46 pseudobonds, 805 residues, 4 models selected

ui tool show "Change Chain IDs"

changechains sel A

Proposed chain ID change would produce multiple residues with the samechain-ID/number/insertion-code combo (A/477/)

select #4/B

1711 atoms, 1755 bonds, 212 residues, 1 model selected

show sel cartoons

show #3 models

hide sel cartoons

select #4/B:402-442

299 atoms, 306 bonds, 41 residues, 1 model selected

show sel cartoons

hide #3 models

select #4/A:402-442

Nothing selected

select #4/C:402-442

Nothing selected

select #4/D:402-442

Nothing selected

select #4/E:402-442

Nothing selected

select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E

3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected

select #4&~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E

3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs"

select #4&~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E

3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected

delete atoms (#!4 & sel)

delete bonds (#!4 & sel)

select #4

3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected

ui tool show "Change Chain IDs"

changechains sel A

Chain IDs of 274 residues changed

changechains sel A

Chain IDs of 0 residues changed

select #4/A

3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

combine #4#5

rename #5 "Stromal ridge and 2fdn"

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs"

select #5/A &protein

2981 atoms, 3061 bonds, 9 pseudobonds, 380 residues, 2 models selected

hide sel atoms

hide #!4 models

select #5/A:27, 31, 504, 807,818, 481, 485, 528

72 atoms, 66 bonds, 8 residues, 1 model selected

show sel atoms

show #!2 models

hide sel atoms

select #2/A:27, 31, 504, 807,818, 481, 485, 528

20 atoms, 18 bonds, 2 residues, 1 model selected

hide #!2 models

show #!1 models

hide #!1 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs"

——— End of log from Sun May 19 17:29:55 2024 ———

opened ChimeraX session

show #!4 models

hide #!4 models

hide #!5 models

show #!5 models

show #3 models

hide #3 models

close #3

show #!2 models

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

rename #2 "PSI chains"

select #5/M

Nothing selected

split #2

Split PSI chains (#2) into 6 models

Chain information for PSI chains A #2.1
Chain	Description
A	No description available

Chain information for PSI chains B #2.2
Chain	Description
B	No description available

Chain information for PSI chains C #2.3
Chain	Description
C	No description available

Chain information for PSI chains D #2.4
Chain	Description
D	No description available

Chain information for PSI chains E #2.5
Chain	Description
E	No description available

Chain information for PSI chains N #2.6
Chain	Description
N	No description available

hide #!2.1 models

hide #!2.2 models

hide #!2.3 models

hide #2.4 models

hide #2.5 models

rename #2 "PSI 6yez chains"

show #!2.1 models

hide #!2.1 models

show #!2.1 models

hide #!2.1 models

show #!4 models

hide #!5 models

hide #!4 models

show #!5 models

hide #!2 models

split #5/B

select #5/B

Nothing selected

show #!2 models

show #!1 models

show #!4 models

hide #!4 models

close #4

rename #5 id 3

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design7.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design6.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design5.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design4.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design3.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design2.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design1.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design0.pdb"

Chain information for best.pdb #4
Chain	Description
A	No description available
B	No description available

Chain information for best_design7.pdb #5
Chain	Description
A	No description available
B	No description available

Chain information for best_design6.pdb #6
Chain	Description
A	No description available
B	No description available

Chain information for best_design5.pdb #7
Chain	Description
A	No description available
B	No description available

Chain information for best_design4.pdb #8
Chain	Description
A	No description available
B	No description available

Chain information for best_design3.pdb #9
Chain	Description
A	No description available
B	No description available

Chain information for best_design2.pdb #10
Chain	Description
A	No description available
B	No description available

Chain information for best_design1.pdb #11
Chain	Description
A	No description available
B	No description available

Chain information for best_design0.pdb #12
Chain	Description
A	No description available
B	No description available

ui tool show Matchmaker

rename #3 "Stromal ridge target"

hide #!3 models

show #!3 models

ui tool show Matchmaker

matchmaker #!4-12 to #3

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker Stromal ridge target, chain A (#3) with best.pdb, chain A (#4), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs: 0.365)

Matchmaker Stromal ridge target, chain A (#3) with best_design7.pdb, chain A (#5), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.362 angstroms; (across all 114 pairs: 0.362)

Matchmaker Stromal ridge target, chain A (#3) with best_design6.pdb, chain A (#6), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs: 0.365)

Matchmaker Stromal ridge target, chain A (#3) with best_design5.pdb, chain A (#7), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs: 0.366)

Matchmaker Stromal ridge target, chain A (#3) with best_design4.pdb, chain A (#8), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.367 angstroms; (across all 114 pairs: 0.367)

Matchmaker Stromal ridge target, chain A (#3) with best_design3.pdb, chain A (#9), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs: 0.366)

Matchmaker Stromal ridge target, chain A (#3) with best_design2.pdb, chain A (#10), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.364 angstroms; (across all 114 pairs: 0.364)

Matchmaker Stromal ridge target, chain A (#3) with best_design1.pdb, chain A (#11), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs: 0.365)

Matchmaker Stromal ridge target, chain A (#3) with best_design0.pdb, chain A (#12), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs: 0.366)

hide #!2 models

hide #!5 models

hide #!6 models

hide #!7 models

hide #!8 models

hide #!9 models

hide #!10 models

hide #!11 models

hide #!12 models

select #4/B:8-11,14-18,38-41,44-48

112 atoms, 108 bonds, 18 residues, 1 model selected

show sel atoms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #13
Chain	Description
A	No description available

ui tool show Matchmaker

matchmaker #13 to #4 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker best.pdb, chain B (#4) with Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb, chain A (#13), sequence alignment score = 242.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: best.pdb #4/B, Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #13/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs: 2.833)

sequence header consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 1

rename #13 Best_alphafold2_rank5.pdb

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb"

Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb #14
Chain	Description
A	No description available

Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #15
Chain	Description
A	No description available

Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #16
Chain	Description
A	No description available

Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #17
Chain	Description
A	No description available

rename #14 Best_alphafold2_rank3.pdb

rename #15 Best_alphafold2_rank1.pdb

rename #16 Best_alphafold2_rank2.pdb

rename #17 Best_alphafold2_rank4.pdb

rename #13 id 18

rename #15 id 13

rename #14 id 15

rename #16 id 14

rename #18 id 17

rename #17.1 id 18

rename #17 id 16

rename #18 id 17

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

ui tool show Matchmaker

matchmaker #13-17 to #4

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank1.pdb, chain A (#13), sequence alignment score = 235.1
RMSD between 34 pruned atom pairs is 0.831 angstroms; (across all 54 pairs: 3.025)

Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank2.pdb, chain A (#14), sequence alignment score = 228.2
RMSD between 32 pruned atom pairs is 0.678 angstroms; (across all 54 pairs: 3.041)

Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank3.pdb, chain A (#15), sequence alignment score = 235.1
RMSD between 32 pruned atom pairs is 0.771 angstroms; (across all 54 pairs: 3.139)

Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank4.pdb, chain A (#16), sequence alignment score = 235.1
RMSD between 34 pruned atom pairs is 0.832 angstroms; (across all 54 pairs: 3.177)

Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank5.pdb, chain A (#17), sequence alignment score = 242.6
RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs: 2.833)

hide #14 models

hide #15 models

hide #16 models

hide #17 models

hide #!3 models

hide #!4 models

select #13/B:8-11,14-18,38-41,44-48

Nothing selected

select #13/A:8-11,14-18,38-41,44-48

112 atoms, 108 bonds, 18 residues, 1 model selected

show #14 models

show #15 models

show #16 models

show #17 models

show sel atoms

hide #17 models

hide #16 models

hide #15 models

hide #14 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

——— End of log from Sat Jun 1 14:26:44 2024 ———

opened ChimeraX session

hide #!1 models

show #!4 models

hide #13 models

show #!3 models

hide #!4 models

help help:user

hide #!3 models

show #!4 models

hide #!4 models

show #!3 models

info #3/A:16 rescolor

Expected a keyword

help help:user

info rescolor #3/A:16

#3/A:16 color #b89a8c

show #!2 models

hide #!3 models

show #!3 models

hide #!3 models

hide #!2.6 models

show #!2.2 models

show #!3 models

hide #!2.2 models

select #3/A &@@color=#b89a8c

Expected a keyword
bad color: b89a8c: Invalid color name or specifier

select #3/A &@@color#b89a8c

Expected a keyword

select #3/A &@@color='#b89a8c'

518 atoms, 413 bonds, 104 residues, 1 model selected

select #3/A &@@color='plum'

Nothing selected

info rescolor #3/A:430

#3/A:430 color #d9b3f5

info rescolor #3/A:804

#3/A:804 color #ebe6fb

info rescolor #3/A:498

#3/A:498 color #b88eb1

info rescolor #3/A:685

#3/A:685 color #c8e69e

select #3/A &@@color='#b89a8c'

518 atoms, 413 bonds, 104 residues, 1 model selected

info residues sel attribute num

info residues #3/A &@@color='#b89a8c' attribute num

info residues #3/A &@@color='#b89a8c' attribute number

residue id #3/A:16 number 16 index 15
residue id #3/A:17 number 17 index 16
residue id #3/A:18 number 18 index 17
residue id #3/A:152 number 152 index 135
residue id #3/A:153 number 153 index 136
residue id #3/A:154 number 154 index 137
residue id #3/A:155 number 155 index 138
residue id #3/A:156 number 156 index 139
residue id #3/A:157 number 157 index 140
residue id #3/A:158 number 158 index 141
residue id #3/A:159 number 159 index 142
residue id #3/A:160 number 160 index 143
residue id #3/A:161 number 161 index 144
residue id #3/A:162 number 162 index 145
residue id #3/A:163 number 163 index 146
residue id #3/A:164 number 164 index 147
residue id #3/A:165 number 165 index 148
residue id #3/A:166 number 166 index 149
residue id #3/A:52 number 52 index 51
residue id #3/A:53 number 53 index 52
residue id #3/A:54 number 54 index 53
residue id #3/A:19 number 19 index 18
residue id #3/A:20 number 20 index 19
residue id #3/A:21 number 21 index 20
residue id #3/A:22 number 22 index 21
residue id #3/A:23 number 23 index 22
residue id #3/A:24 number 24 index 23
residue id #3/A:25 number 25 index 24
residue id #3/A:26 number 26 index 25
residue id #3/A:27 number 27 index 26
residue id #3/A:28 number 28 index 27
residue id #3/A:29 number 29 index 28
residue id #3/A:30 number 30 index 29
residue id #3/A:31 number 31 index 30
residue id #3/A:32 number 32 index 31
residue id #3/A:33 number 33 index 32
residue id #3/A:34 number 34 index 33
residue id #3/A:35 number 35 index 34
residue id #3/A:36 number 36 index 35
residue id #3/A:37 number 37 index 36
residue id #3/A:38 number 38 index 37
residue id #3/A:39 number 39 index 38
residue id #3/A:40 number 40 index 39
residue id #3/A:41 number 41 index 40
residue id #3/A:42 number 42 index 41
residue id #3/A:43 number 43 index 42
residue id #3/A:44 number 44 index 43
residue id #3/A:45 number 45 index 44
residue id #3/A:46 number 46 index 45
residue id #3/A:47 number 47 index 46
residue id #3/A:48 number 48 index 47
residue id #3/A:49 number 49 index 48
residue id #3/A:50 number 50 index 49
residue id #3/A:51 number 51 index 50
residue id #3/A:209 number 209 index 184
residue id #3/A:210 number 210 index 185
residue id #3/A:211 number 211 index 186
residue id #3/A:212 number 212 index 187
residue id #3/A:213 number 213 index 188
residue id #3/A:214 number 214 index 189
residue id #3/A:215 number 215 index 190
residue id #3/A:216 number 216 index 191
residue id #3/A:217 number 217 index 192
residue id #3/A:218 number 218 index 193
residue id #3/A:219 number 219 index 194
residue id #3/A:220 number 220 index 195
residue id #3/A:221 number 221 index 196
residue id #3/A:222 number 222 index 197
residue id #3/A:223 number 223 index 198
residue id #3/A:224 number 224 index 199
residue id #3/A:225 number 225 index 200
residue id #3/A:226 number 226 index 201
residue id #3/A:167 number 167 index 150
residue id #3/A:168 number 168 index 151
residue id #3/A:169 number 169 index 152
residue id #3/A:170 number 170 index 153
residue id #3/A:171 number 171 index 154
residue id #3/A:172 number 172 index 155
residue id #3/A:173 number 173 index 156
residue id #3/A:174 number 174 index 157
residue id #3/A:175 number 175 index 158
residue id #3/A:176 number 176 index 159
residue id #3/A:177 number 177 index 160
residue id #3/A:178 number 178 index 161
residue id #3/A:179 number 179 index 162
residue id #3/A:180 number 180 index 163
residue id #3/A:181 number 181 index 164
residue id #3/A:182 number 182 index 165
residue id #3/A:183 number 183 index 166
residue id #3/A:194 number 194 index 169
residue id #3/A:195 number 195 index 170
residue id #3/A:196 number 196 index 171
residue id #3/A:197 number 197 index 172
residue id #3/A:198 number 198 index 173
residue id #3/A:199 number 199 index 174
residue id #3/A:200 number 200 index 175
residue id #3/A:201 number 201 index 176
residue id #3/A:202 number 202 index 177
residue id #3/A:203 number 203 index 178
residue id #3/A:204 number 204 index 179
residue id #3/A:205 number 205 index 180
residue id #3/A:206 number 206 index 181
residue id #3/A:207 number 207 index 182
residue id #3/A:208 number 208 index 183

info residues sel attribute number

info residues #3/A &@@color='#b89a8c' attribute number

show #!4 models

hide #!3 models

show #!3 models

select #4/A:1-227

857 atoms, 885 bonds, 2 pseudobonds, 108 residues, 2 models selected

ui tool show "Color Actions"

color sel tan

hide #!3 models

show #!3 models

select #4/A:425-436

Nothing selected

hide #!3 models

select #4/A:410-421

76 atoms, 77 bonds, 12 residues, 1 model selected

color sel peru

select #4/A:456-535

611 atoms, 624 bonds, 80 residues, 1 model selected

show #!3 models

hide #!3 models

color sel violet

select #4/A:572-685

908 atoms, 934 bonds, 114 residues, 1 model selected

color sel light steel blue

color sel powder blue

color sel sky blue

color sel medium orchid

color sel light pink

color sel light coral

color sel light pink

select #4/A:749-814

528 atoms, 540 bonds, 66 residues, 1 model selected

color sel light coral

show #!1 models

show #!2.3 models

show #!2.1 models

hide #!2.1 models

hide #!2.3 models

show #!3 models

hide #!3 models

show #!2.1 models

show #!2.3 models

show #2.4 models

show #2.5 models

select #2/A:1-16

130 atoms, 132 bonds, 16 residues, 1 model selected

hide sel cartoons

select #2/A:1-16,54-58

170 atoms, 171 bonds, 21 residues, 1 model selected

select #2/A:1-16,54-146

809 atoms, 828 bonds, 3 pseudobonds, 97 residues, 2 models selected

hide sel cartoons

select #2:SF4 :<3 &#2/A-E

109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected

hide #!1 models

hide #!4 models

show #!2.2 models

show #!3 models

select add #2.2

1804 atoms, 1850 bonds, 14 pseudobonds, 226 residues, 6 models selected

show sel cartoons

hide sel cartoons

select subtract #2.2

93 atoms, 95 bonds, 9 pseudobonds, 14 residues, 4 models selected

select #2/B:425-436

76 atoms, 77 bonds, 12 residues, 1 model selected

show sel cartoons

hide #!3 models

show #!3 models

hide #!3 models

show #!3 models

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

hide #!3 models

select #2:SF4 :<3 &#2/A-E

109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected

select #2:SF4 :<3 &#2/A-E

109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected

show sel atoms

color sel byhetero

show sel cartoons

show #!4 models

select #4/A:456-535

611 atoms, 624 bonds, 80 residues, 1 model selected

hide #!2.2 models

hide #!2.1 models

hide #2.4 models

hide #2.5 models

ui tool show Matchmaker

matchmaker #!4 & sel to #2.3/C pairing bs showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI chains C, chain C (#2.3) with best.pdb, chain A (#4), sequence alignment score = 401
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: PSI chains C #2.3/C, best.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs: 0.395)

show #!2.1 models

hide #!2.1 models

show #!2.1 models

show #!2.2 models

select #4/A:CYS

84 atoms, 70 bonds, 14 residues, 1 model selected

show sel atoms

color sel byhetero

hide #!2 models

show #!2 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

split #2.1 atoms :SF4

Split PSI chains A (#2.1) into 2 models

Chain information for PSI chains A 2 #2.1.2
Chain	Description
A	No description available

hide #!2.1.2 models

split #2.3 atoms :SF4

Split PSI chains C (#2.3) into 2 models

Chain information for PSI chains C 2 #2.3.2
Chain	Description
C	No description available

Associated PSI chains C 2 (2.3.2) chain C to best.pdb, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: PSI chains C 2 #2.3.2/C, best.pdb #4/A

hide #2.3.2 models

hide #2.3.1 models

show #2.3.1 models

hide #2.3.1 models

show #2.3.1 models

rename #3 id 20

combine #2.1.1#2.3.1

hide #!2 models

rename #3 "Fe4S4 clusters"

show #!1 models

select #1 &!@@color='lime'

Expected a keyword

select #1 &~@@color='lime'

669 atoms, 451 bonds, 8 pseudobonds, 151 residues, 2 models selected

color sel orange

color sel dark orange

color sel byhetero

select #1 &H

272 atoms, 48 residues, 1 model selected

hide sel atoms

select #1

762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected

color sel byhetero

combine #1

hide #!1 models

ui tool show Matchmaker

matchmaker #!18 to #4/B pairing bs showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker best.pdb, chain B (#4) with copy of 2fdn, chain M (#18), sequence alignment score = 157.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: best.pdb #4/B, copy of 2fdn #18/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 38 pruned atom pairs is 0.829 angstroms; (across all 51 pairs: 2.274)

select #4:CYS

132 atoms, 110 bonds, 22 residues, 1 model selected

select #4/B:CYS

48 atoms, 40 bonds, 8 residues, 1 model selected

show #!5 models

hide #!4 models

hide #!5 models

show #!4 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

show #!5 models

hide #!5 models

help help:user

color #5-18/A:1-227 tan

color #5-18/A:410-421 peru

color #5-18/A:456-535 violet

color #5-18/A:572-685 light pink

color #5-18/A:749-814 light coral

show #!5 models

hide #!4 models

hide #!5 models

show #!6 models

hide #!6 models

show #!7 models

hide #!7 models

show #!8 models

hide #!8 models

show #!9 models

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show #!10 models

show #!9 models

show #!7 models

show #!8 models

show #!6 models

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hide #3 models

show #!4 models

show #3 models

show #!11 models

show #!12 models

show #13 models

show #14 models

show #15 models

hide #15 models

hide #14 models

show #14 models

hide #14 models

hide #13 models

close #13-17

hide #!5 models

hide #!6 models

hide #!7 models

hide #!8 models

hide #!9 models

hide #!10 models

hide #!11 models

hide #!12 models

hide #!18 models

show #!5 models

show #!6 models

show #!7 models

show #!8 models

show #!9 models

show #!10 models

show #!11 models

show #!12 models

select add #4

3337 atoms, 3419 bonds, 6 pseudobonds, 434 residues, 2 models selected

select subtract #4

Nothing selected

ui tool show Matchmaker

help help:user

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

select #1:CYS

80 atoms, 72 bonds, 8 residues, 1 model selected

align #18:CYS toAtoms #4:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.311 angstroms

align #18:CYS toAtoms #1:CYS matchAtomNames true move nothing

RMSD between 80 atom pairs is 0.000 angstroms

align #18:CYS toAtoms #5:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.316 angstroms

align #18:CYS toAtoms #6:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.305 angstroms

align #18:CYS toAtoms #7:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.308 angstroms

align #18:CYS toAtoms #8:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.316 angstroms

align #18:CYS toAtoms #9:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.306 angstroms

align #18:CYS toAtoms #10:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.309 angstroms

align #18:CYS toAtoms #11:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.311 angstroms

align #18:CYS toAtoms #12:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.309 angstroms

select #5-12

26753 atoms, 27419 bonds, 48 pseudobonds, 3472 residues, 16 models selected

select #5-12/B:CYS

384 atoms, 320 bonds, 64 residues, 8 models selected

show sel atoms

color sel byhetero

align #18:CYS toAtoms #4/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.745 angstroms

align #18:CYS toAtoms #5/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.738 angstroms

align #18:CYS toAtoms #6/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.898 angstroms

align #18:CYS toAtoms #7/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.823 angstroms

align #18:CYS toAtoms #8/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.953 angstroms

align #18:CYS toAtoms #9/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.867 angstroms

align #18:CYS toAtoms #10/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.898 angstroms

align #18:CYS toAtoms #11/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.745 angstroms

align #18:CYS toAtoms #12/B:CYS matchAtomNames true move nothing

Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.874 angstroms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

——— End of log from Tue Jun 4 18:24:08 2024 ———

opened ChimeraX session

hide #!12 models

hide #!10 models

hide #!9 models

hide #!8 models

hide #!7 models

hide #!6 models

show #!18 models

hide #!5 models

hide #!4 models

hide #!11 models

select #18/A:CYS

Nothing selected

select #18/A:CYS

Nothing selected

select #18:CYS

80 atoms, 72 bonds, 8 residues, 1 model selected

ui tool show "Color Actions"

color sel cyan

color sel byhetero

select #4/B:CYS

48 atoms, 40 bonds, 8 residues, 1 model selected

show #3#!18 atoms

hide #3#!18 atoms

select #3

24 atoms, 36 bonds, 3 residues, 1 model selected

show sel atoms

select #18:CYS

80 atoms, 72 bonds, 8 residues, 1 model selected

show sel atoms

544 atoms, 96 residues, 2 models selected

hide sel & #!18 atoms

select #18:FS4

Nothing selected

select #18:SF4

16 atoms, 24 bonds, 2 residues, 1 model selected

show sel atoms

select add #18

762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected

select subtract #18

Nothing selected

show #!4 models

select #4/B:CYS

48 atoms, 40 bonds, 8 residues, 1 model selected

hide #!4 models

show #!5 models

show #!11 models

hide #!5 models

show #!5 models

show #!4 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs"

——— End of log from Tue Jun 4 19:01:21 2024 ———

opened ChimeraX session

hide #3 models

hide #!5 models

hide #!18 models

hide #!11 models

show #!11 models

hide #!11 models

show #!12 models

hide #!12 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta"

Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta

notes

Opened 64 sequences from design.fasta

show #!11 models

ui tool show Matchmaker

matchmaker #11/B to #4/B pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker best.pdb, chain B (#4) with best_design1.pdb, chain B (#11), sequence alignment score = 287.3
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: best.pdb #4/B, best_design1.pdb #11/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 54 pruned atom pairs is 0.000 angstroms; (across all 54 pairs: 0.000)

sequence header 2 consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 2

rename #4 "best (best design1).pdb"

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!2 models

hide #!2.1 models

show #!2.1 models

show #2.5 models

show #!2.6 models

hide #!2.6 models

show #2.4 models

hide #2.5 models

hide #2.4 models

show #3 models

hide #!2 models

select #4/B:53-54 #11/B:53-54

28 atoms, 26 bonds, 4 residues, 2 models selected

select #4/B:24-54 #11/B:24-54

418 atoms, 418 bonds, 62 residues, 2 models selected

[Repeated 1 time(s)]

select add #11/B:1

5 atoms, 4 bonds, 1 residue, 1 model selected

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs"

——— End of log from Thu Sep 19 17:01:48 2024 ———

opened ChimeraX session

hide #3 models

show #3 models

hide #3 models

show #3 models

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hide #!2 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!11 models

show #!1 models

hide #!1 models

show #!18 models

show #!2 models

hide #!2 models

show #!2 models

hide #!2 models

hide #3 models

show #3 models

close #2

Cell requested for row 10 is out of bounds for table with 14 rows! Resizing table model.

show #!11 models

hide #!11 models

Cell requested for row 2 is out of bounds for table with 14 rows! Resizing table model.

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

show #!5 models

hide #!5 models

show #!11 models

hide #!4 models

show #!4 models

show #!20 models

hide #!20 models

hide #!11 models

close #5-12

show #!1 models

ui tool show Matchmaker

matchmaker #1/M to #4/B pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker best (best design1).pdb, chain B (#4) with 2fdn, chain M (#1), sequence alignment score = 157.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 2fdn #1/M, best (best design1).pdb #4/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 40 pruned atom pairs is 0.905 angstroms; (across all 51 pairs: 2.218)

sequence header 1 consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 1

select #4/B:9

4 atoms, 3 bonds, 1 residue, 1 model selected

select #4/B:9

4 atoms, 3 bonds, 1 residue, 1 model selected

select #4/B:9

4 atoms, 3 bonds, 1 residue, 1 model selected

select #4/B:9

4 atoms, 3 bonds, 1 residue, 1 model selected

show sel atoms

select #4/B:9,23-30

64 atoms, 62 bonds, 9 residues, 1 model selected

select #4/B:9,23-32

77 atoms, 75 bonds, 11 residues, 1 model selected

hide #!18 models

hide #3 models

hide #!1 models

ui tool show Contacts

select #4/B

357 atoms, 359 bonds, 54 residues, 1 model selected

contacts sel restrict #4/A resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

22 contacts
                 atom1                                    atom2                    overlap  distance
best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 NH2   0.873    2.647
best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 CB    0.734    2.566
best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 OG1   0.578    1.902
best (best design1).pdb #4/B GLY 10 O    best (best design1).pdb #4/A ILE 466 CD1   0.308    2.992
best (best design1).pdb #4/B GLU 16 CD   best (best design1).pdb #4/A THR 802 OG1   0.249    3.091
best (best design1).pdb #4/B GLU 30 CG   best (best design1).pdb #4/A LYS 489 CE    0.245    3.515
best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 CZ    0.119    3.371
best (best design1).pdb #4/B CYS 11 CA   best (best design1).pdb #4/A ILE 466 CD1   0.070    3.690
best (best design1).pdb #4/B GLU 16 CD   best (best design1).pdb #4/A THR 802 CB    -0.041    3.801
best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 NH1   -0.058    3.578
best (best design1).pdb #4/B VAL 25 CG2  best (best design1).pdb #4/A VAL 776 CG1   -0.063    3.823
best (best design1).pdb #4/B GLU 30 CG   best (best design1).pdb #4/A LYS 489 NZ    -0.072    3.592
best (best design1).pdb #4/B GLU 30 OE1  best (best design1).pdb #4/A LYS 489 CE    -0.103    3.403
best (best design1).pdb #4/B GLY 10 O    best (best design1).pdb #4/A ILE 466 CG1   -0.116    3.416
best (best design1).pdb #4/B CYS 11 CB   best (best design1).pdb #4/A CYS 468 SG    -0.142    3.792
best (best design1).pdb #4/B GLU 30 CD   best (best design1).pdb #4/A LYS 489 CE    -0.168    3.928
best (best design1).pdb #4/B GLU 30 CD   best (best design1).pdb #4/A LYS 489 NZ    -0.185    3.705
best (best design1).pdb #4/B GLU 46 OE1  best (best design1).pdb #4/A ARG 12 NH1    -0.272    2.932
best (best design1).pdb #4/B GLU 26 CG   best (best design1).pdb #4/A ALA 777 CB    -0.283    4.043
best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 CA    -0.299    3.599
best (best design1).pdb #4/B ALA 7 CA    best (best design1).pdb #4/A ARG 473 NH2   -0.367    3.887
best (best design1).pdb #4/B VAL 25 CG1  best (best design1).pdb #4/A VAL 789 CG1   -0.391    4.151

22 contacts

hide #4.2 models

show #4.2 models

select add #4.2

357 atoms, 359 bonds, 22 pseudobonds, 54 residues, 2 models selected

select subtract #4.2

357 atoms, 359 bonds, 54 residues, 1 model selected

hide #4.2 models

show #4.2 models

select #4/B:7,10-11,16,25-26,30/A:473,802,466,489,776-777,468,12,789

120 atoms, 107 bonds, 21 pseudobonds, 16 residues, 2 models selected

style sel ball

Changed 120 atom styles

color sel byhetero

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 16 items

name frozen contacts sel

select #4/B

357 atoms, 359 bonds, 54 residues, 1 model selected

ui tool show Clashes

clashes sel restrict #4/A resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

2 clashes
                 atom1                                    atom2                    overlap  distance
best (best design1).pdb #4/B ALA 7 CB    best (best design1).pdb #4/A ARG 473 NH2   0.873    2.647
best (best design1).pdb #4/B GLU 16 OE1  best (best design1).pdb #4/A THR 802 CB    0.734    2.566

2 clashes

select #4/B:7,16

14 atoms, 12 bonds, 2 residues, 1 model selected

select #4/B

357 atoms, 359 bonds, 54 residues, 1 model selected

ui tool show H-Bonds

hbonds sel color #0096ff restrict #4/A interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	4 best (best design1).pdb

4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
best (best design1).pdb #4/A ARG 12 NH1   best (best design1).pdb #4/B GLU 46 OE1  no hydrogen  2.932  N/A
best (best design1).pdb #4/A LYS 489 NZ   best (best design1).pdb #4/B GLU 26 O    no hydrogen  3.483  N/A
best (best design1).pdb #4/A LYS 489 NZ   best (best design1).pdb #4/B GLU 30 OE1  no hydrogen  3.116  N/A
best (best design1).pdb #4/A THR 802 OG1  best (best design1).pdb #4/B GLU 16 OE1  no hydrogen  1.902  N/A

4 hydrogen bonds found

select #4/B:46,26,30,16/A:12,489,802

63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected

style sel ball

Changed 63 atom styles

hide #4.2 models

hide #4.3 models

select #4/B:46,26,30,16/A:12,489,802

63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected

select #4/B:1-6,10-23,33-48,51-54 #1/M:1-6,10-23,32-47,52-55

755 atoms, 754 bonds, 80 residues, 2 models selected

select #4/B:46,26,30,16/A:12,489,802

63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected

select contacts &~#4/B:46,26,30,16/A:12,489,802

66 atoms, 58 bonds, 11 pseudobonds, 10 residues, 3 models selected

style sel sphere

Changed 66 atom styles

color sel byhetero

[Repeated 1 time(s)]

select #4/B:26 &~backbone

5 atoms, 4 bonds, 1 residue, 1 model selected

style sel sphere

Changed 5 atom styles

show #4.2 models

style sel ball

Changed 5 atom styles

hide #4.4 models

show #4.4 models

hide #4.2 models

show #4.2 models

hide #4.2 models

select #4/B:26 &~backbone

5 atoms, 4 bonds, 1 residue, 1 model selected

style sel sphere

Changed 5 atom styles

surface #4/A

surface #4/B

coulombic #4/B surfaces #4.6

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for best (best design1).pdb_B SES surface #4.6: minimum, -17.76, mean -5.37, maximum 4.03

coulombic #4/A surfaces #4.5

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for best (best design1).pdb_A SES surface #4.5: minimum, -15.01, mean 1.13, maximum 14.51

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

open 6yez

6yez title:
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]

Chain information for 6yez #2
Chain	Description	UniProt
1	Lhca1
2	Chlorophyll a-b binding protein, chloroplastic	Q41038_PEA 58-265
3	Chlorophyll a-b binding protein 3, chloroplastic	CB23_PEA 55-275
4	Chlorophyll a-b binding protein P4, chloroplastic	CB24_PEA 52-249
A	Photosystem I P700 chlorophyll a apoprotein A1	A0A0F6NFW5_PEA 16-758
B	Photosystem I P700 chlorophyll a apoprotein A2	A0A0F6NGI2_PEA 2-734
C	Photosystem I iron-sulfur center	PSAC_PEA 2-81
D	PsaD
E	PsaE
F	PsaF
G	PsaG
H	PsaH
I	Photosystem I reaction center subunit VIII	PSAI_PEA 2-32
J	PsaJ
K	Photosystem I reaction center subunit X psaK	E1C9L3_PEA 46-126
L	PsaL
N	Ferredoxin-1, chloroplastic	FER1_PEA 1-97
P	Plastocyanin, chloroplastic	PLAS_PEA 1-99

Non-standard residues in 6yez #2
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
C7Z — (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol ((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT — (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-β,β-carotene-3,3'-diol (violaxanthin)

select #2 &protein

26851 atoms, 27685 bonds, 3438 residues, 1 model selected

hide sel cartoons

hide sel atoms

show sel cartoons

hide #4.6 models

hide #4.5 models

ui tool show Matchmaker

matchmaker #2/C to #4/A pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker best (best design1).pdb, chain A (#4) with 6yez, chain C (#2), sequence alignment score = 401
RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs: 0.395)

show #4.6 models

hide #4.6 models

show #4.6 models

hide #4.6 models

show #4.6 models

hide #4.6 models

show #4.5 models

hide #4.5 models

coulombic #2/E

The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
6yez #2/E LYS 129 OXT

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_E SES surface #2.2: minimum, -13.31, mean 0.69, maximum 9.65

hide #!4 models

coulombic #2/C:2-81

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30, maximum 9.66

coulombic #2/D

The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
6yez #2/D LEU 211 OXT

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16, maximum 13.86

toolshed show

volume showOutlineBox true

No volumes specified

show #3 models

show #!4 models

select #2/N/P

1457 atoms, 1483 bonds, 7 pseudobonds, 198 residues, 2 models selected

hide sel cartoons

hide sel atoms

select #2:3001

8 atoms, 12 bonds, 1 residue, 1 model selected

cofr sel

select #4/A

2980 atoms, 3060 bonds, 6 pseudobonds, 380 residues, 2 models selected

hide sel cartoons

select contacts :<1 &#2

128 atoms, 118 bonds, 17 residues, 1 model selected

show sel atoms

hide sel atoms

hide #2.4 models

hide #2.3 models

hide #2.2 models

select #4/A

2980 atoms, 3060 bonds, 7 pseudobonds, 380 residues, 3 models selected

show sel cartoons

show #4.5 models

show #4.6 models

select #2:CA,CU,DGD,3PH,C7Z,LHG

739 atoms, 735 bonds, 20 residues, 1 model selected

select #2/1

2580 atoms, 2690 bonds, 61 pseudobonds, 214 residues, 2 models selected

select #2/1-4

10673 atoms, 11130 bonds, 241 pseudobonds, 907 residues, 2 models selected

hide sel cartoons

hide sel atoms

select #2/C-E

2288 atoms, 2352 bonds, 7 pseudobonds, 291 residues, 2 models selected

hide sel cartoons

set bgColor white

graphics silhouettes true

hide #!4 models

show #!4 models

hide #4.4 models

hide #4.5 models

show #4.4 models

hide #4.6 models

show #4.5 models

hide #4.5 models

surface #2 enclose #2/A-B/F-L

close #2.5

select contacts :<1 &#2

128 atoms, 118 bonds, 17 residues, 1 model selected

select #4/A :<1 &#2

3059 atoms, 3141 bonds, 4 pseudobonds, 382 residues, 2 models selected

select #4/A :<1 &#2 &protein

2994 atoms, 3072 bonds, 381 residues, 1 model selected

name frozen minAB sel

select #2/A-B/F-L &~minAB

23858 atoms, 24789 bonds, 418 pseudobonds, 2167 residues, 2 models selected

surface #2 enclose #2/A-B/F-L &~minAB

show #4.5 models

show #4.6 models

hide #4.6 models

select #1:SF4

16 atoms, 24 bonds, 2 residues, 1 model selected

show #!1 models

select #1:1-55

652 atoms, 657 bonds, 55 residues, 1 model selected

hide sel cartoons

hide sel atoms

select #4/A &contacts

71 atoms, 63 bonds, 9 residues, 1 model selected

style sel stick

Changed 71 atom styles

select :CL0,CLA

8422 atoms, 8990 bonds, 568 pseudobonds, 142 residues, 2 models selected

color (#!2 & sel) lime

color sel byhetero

Cell requested for row 8 is out of bounds for table with 17 rows! Resizing table model.

select add #4.5

2980 atoms, 380 residues, 1 model selected

transparency (#!4 & sel) 30

transparency (#!4 & sel) 20

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

view name front

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png" width 845 height 690 supersample 3 transparentBackground true

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png" width 1470 height 1200 supersample 3 transparentBackground true

select contacts

120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected

style sel stick

Changed 120 atom styles

show #4.6 models

select add #4.6

357 atoms, 54 residues, 1 model selected

transparency (#!4 & sel) 20

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png" width 1470 height 1200 supersample 3 transparentBackground true

hide #4.5 models

hide #4.6 models

select contacts

120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected

style sel sphere

Changed 120 atom styles

show #4.5 models

hide #4.5 models

show #4.5 models

hide #4.5 models

show #4.6 models

select #4/B &contacts

49 atoms, 44 bonds, 7 residues, 1 model selected

style sel stick

Changed 49 atom styles

view name back

show #4.5 models

hide #4.5 models

hide #4.6 models

show #4.6 models

hide #4.6 models

select #4/A:489

9 atoms, 8 bonds, 1 residue, 1 model selected

style sel stick

Changed 9 atom styles

show #4.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png" width 1470 height 1200 supersample 3 transparentBackground true

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png" width 1470 height 1200 supersample 3 transparentBackground true

view front

select #4/A:12

11 atoms, 10 bonds, 1 residue, 1 model selected

style sel stick

Changed 11 atom styles

show #4.5 models

hide #4.6 models

select #4/B:16,30,46

27 atoms, 24 bonds, 3 residues, 1 model selected

style sel ball

Changed 27 atom styles

select #4/B:26 &backbone

4 atoms, 3 bonds, 1 residue, 1 model selected

style sel ball

Changed 4 atom styles

view front

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

hide #4.5 models

select #4/A &contacts &~489,802

Expected a keyword

select #4/A &contacts &~:489,802

55 atoms, 49 bonds, 7 residues, 1 model selected

style sel stick

Changed 55 atom styles

select #4/A:12,489,802

27 atoms, 24 bonds, 3 residues, 1 model selected

style sel ball

Changed 27 atom styles

show #4.5 models

hide #4.5 models

show #4.5 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

hide #4.5 models

show #4.5 models

select #4/B:16,26,30,46/A:12,489,802

63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected

name frozen hBonds sel

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

select #4/B &contacts &~hBonds

22 atoms, 19 bonds, 4 residues, 1 model selected

style sel sphere

Changed 22 atom styles

select #4/B:26 &~backbone

5 atoms, 4 bonds, 1 residue, 1 model selected

style sel sphere

Changed 5 atom styles

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png" width 1568 height 1280 supersample 3 transparentBackground true

select #4/B &contacts &~hBonds

22 atoms, 19 bonds, 4 residues, 1 model selected

style sel stick

Changed 22 atom styles

select #4/B:26 &~backbone

5 atoms, 4 bonds, 1 residue, 1 model selected

style sel stick

Changed 5 atom styles

show #4.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png" width 1568 height 1280 supersample 3 transparentBackground true

hide #4.6 models

hide #4.5 models

show #4.6 models

view back

select #4/A &contacts &~hBonds

44 atoms, 39 bonds, 6 residues, 1 model selected

style sel sphere

Changed 44 atom styles

select minAB

3213 atoms, 3072 bonds, 410 residues, 1 model selected

hide sel cartoons

hide sel atoms

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png" width 1568 height 1280 supersample 3 transparentBackground true

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs"

——— End of log from Mon Sep 30 14:03:27 2024 ———

opened ChimeraX session

Chain information for relaxed_structure.pdb #5
Chain	Description
A	No description available
B	No description available

ui tool show Matchmaker

hide #5 models

show #5 models

ui tool show Matchmaker

matchmaker #5/A to #2/C pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6yez, chain C (#2) with relaxed_structure.pdb, chain A (#5), sequence alignment score = 364.4
RMSD between 73 pruned atom pairs is 0.691 angstroms; (across all 80 pairs: 2.602)

hide #!4 models

hide #!2 models

close #5

show #!4 models

Chain information for relaxed_structure.pdb #5
Chain	Description
A	No description available
B	No description available
C	No description available
D	No description available
E	No description available
F	No description available

select #5 &protein

28495 atoms, 28969 bonds, 1826 residues, 1 model selected

hide sel atoms

show sel cartoons

hide #!4 models

hide #!1 models

show #!2 models

view front

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

hide #2.5 models

hide #!2 models

surface #5

show #!2 models

coulombic #5/A surfaces #5.1

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum, -11.84, mean -0.24, maximum 17.92

coulombic #5/B surfaces #5.2

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum, -13.17, mean 0.31, maximum 13.60

coulombic #5/C surfaces #5.3

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum, -14.28, mean 0.87, maximum 12.27

coulombic #5/D surfaces #5.4

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85, mean 2.10, maximum 15.14

coulombic #5/E surfaces #5.5

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum, -10.97, mean 1.53, maximum 12.30

coulombic #5/F surfaces #5.6

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum, -13.89, mean -3.67, maximum 7.01

select add #5.1

11581 atoms, 743 residues, 1 model selected

select add #5.2

23096 atoms, 1476 residues, 2 models selected

select add #5.3

24310 atoms, 1556 residues, 3 models selected

select add #5.4

26587 atoms, 1699 residues, 4 models selected

select add #5.5

27646 atoms, 1765 residues, 5 models selected

select subtract #5.4

25369 atoms, 1622 residues, 6 models selected

select subtract #5.5

24310 atoms, 1556 residues, 5 models selected

select add #5.6

25159 atoms, 1617 residues, 4 models selected

select add #5.4

27436 atoms, 1760 residues, 5 models selected

select add #5.5

28495 atoms, 1826 residues, 6 models selected

transparency (#!5 & sel) 20

show #!1 models

hide #5.6 models

select #5/C/F &:Cys &~H

102 atoms, 85 bonds, 17 residues, 1 model selected

show sel atoms

color sel byhetero

style sel stick

Changed 102 atom styles

select #5/F#1/M &:CYS

168 atoms, 152 bonds, 16 residues, 2 models selected

ui tool show Matchmaker

matchmaker #1/M & sel to #5/F & sel pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#1), sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)

select #5/A-E

27646 atoms, 28113 bonds, 1765 residues, 1 model selected

ui tool show Clashes

clashes sel restrict #5/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

0 clashes
atom1  atom2  overlap  distance

No clashes

ui tool show Contacts

contacts sel restrict #15/B resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

0 contacts
atom1  atom2  overlap  distance

No contacts

contacts sel restrict #5/F resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

160 contacts
                atom1                                   atom2                   overlap  distance
relaxed_structure.pdb #5/C ARG 18 HH11  relaxed_structure.pdb #5/F GLU 17 CD     0.421    2.279
relaxed_structure.pdb #5/D LYS 109 HZ2  relaxed_structure.pdb #5/F GLU 19 CD     0.387    2.313
relaxed_structure.pdb #5/E THR 54 HG1   relaxed_structure.pdb #5/F GLU 9 OE2     0.371    1.709
relaxed_structure.pdb #5/D LYS 109 HZ2  relaxed_structure.pdb #5/F GLU 19 OE1    0.357    1.723
relaxed_structure.pdb #5/A LYS 31 HZ2   relaxed_structure.pdb #5/F ASP 30 OD2    0.353    1.727
relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 OD1    0.348    1.732
relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F GLU 19 CD     0.340    2.985
relaxed_structure.pdb #5/E ARG 43 HH21  relaxed_structure.pdb #5/F GLU 9 OE1     0.335    1.745
relaxed_structure.pdb #5/E THR 54 HG1   relaxed_structure.pdb #5/F GLU 9 CD      0.326    2.374
relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F GLU 17 OE2    0.323    1.757
relaxed_structure.pdb #5/A ARG 27 HH11  relaxed_structure.pdb #5/F ASP 30 OD1    0.313    1.767
relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 HH22   0.308    1.772
relaxed_structure.pdb #5/E ARG 43 HH22  relaxed_structure.pdb #5/F ALA 7 O       0.213    1.867
relaxed_structure.pdb #5/C PRO 58 CB    relaxed_structure.pdb #5/F ILE 11 CD1    0.169    3.231
relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 CG     0.166    2.534
relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F THR 8 HA      0.161    2.464
relaxed_structure.pdb #5/A THR 28 OG1   relaxed_structure.pdb #5/F ARG 32 HE     0.158    1.942
relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 N      0.152    3.098
relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 HH12   0.146    1.934
relaxed_structure.pdb #5/D LYS 109 HZ1  relaxed_structure.pdb #5/F PRO 18 O      0.146    1.934
relaxed_structure.pdb #5/C ARG 18 HH11  relaxed_structure.pdb #5/F GLU 17 OE1    0.136    1.944
relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F PRO 18 HG2    0.085    2.540
relaxed_structure.pdb #5/C ARG 18 NH1   relaxed_structure.pdb #5/F GLU 17 CD     0.062    3.263
relaxed_structure.pdb #5/A ARG 27 CZ    relaxed_structure.pdb #5/F ASP 30 OD1    0.055    3.125
relaxed_structure.pdb #5/C ARG 18 HH11  relaxed_structure.pdb #5/F GLU 17 OE2    0.055    2.025
relaxed_structure.pdb #5/D LYS 109 HZ3  relaxed_structure.pdb #5/F GLU 19 OE2    0.047    2.033
relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 OD1    0.038    2.667
relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F SER 12 O      0.034    3.146
relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F GLU 19 OE1    0.032    2.673
relaxed_structure.pdb #5/C ALA 35 CB    relaxed_structure.pdb #5/F VAL 51 HA     0.028    2.672
relaxed_structure.pdb #5/A LYS 31 NZ    relaxed_structure.pdb #5/F ASP 30 OD2    0.025    2.680
relaxed_structure.pdb #5/A ARG 27 NH1   relaxed_structure.pdb #5/F ASP 30 OD1    0.020    2.685
relaxed_structure.pdb #5/C LYS 34 C     relaxed_structure.pdb #5/F GLY 50 O      0.019    3.161
relaxed_structure.pdb #5/C PRO 58 CG    relaxed_structure.pdb #5/F ILE 11 CD1    0.015    3.385
relaxed_structure.pdb #5/C ILE 11 CD1   relaxed_structure.pdb #5/F PRO 53 HB3    0.012    2.688
relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F GLU 19 OE2    0.011    2.694
relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F GLU 9 CD      -0.001    3.201
relaxed_structure.pdb #5/A ARG 27 HH11  relaxed_structure.pdb #5/F ASP 30 CG     -0.002    2.702
relaxed_structure.pdb #5/C THR 14 HG1   relaxed_structure.pdb #5/F ALA 15 HB3    -0.006    2.006
relaxed_structure.pdb #5/C CYS 13 O     relaxed_structure.pdb #5/F ALA 15 HB3    -0.012    2.492
relaxed_structure.pdb #5/D LYS 109 HZ3  relaxed_structure.pdb #5/F GLU 19 CD     -0.015    2.715
relaxed_structure.pdb #5/C PRO 58 HG3   relaxed_structure.pdb #5/F ILE 11 CD1    -0.017    2.717
relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 NH2    -0.023    2.728
relaxed_structure.pdb #5/C PRO 58 CB    relaxed_structure.pdb #5/F ILE 11 HD11   -0.027    2.727
relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F GLU 17 OE2    -0.028    2.733
relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F GLU 9 OE1     -0.044    2.749
relaxed_structure.pdb #5/C ARG 18 CZ    relaxed_structure.pdb #5/F GLY 14 O      -0.062    3.242
relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F GLU 17 CD     -0.064    2.764
relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 CG     -0.076    3.401
relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 CZ     -0.080    3.260
relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F GLU 9 OE2     -0.082    2.662
relaxed_structure.pdb #5/A ASP 34 CG    relaxed_structure.pdb #5/F ARG 32 HH12   -0.083    2.783
relaxed_structure.pdb #5/A LYS 31 HZ2   relaxed_structure.pdb #5/F ASP 30 CG     -0.084    2.784
relaxed_structure.pdb #5/E SER 53 C     relaxed_structure.pdb #5/F GLU 9 OE2     -0.087    3.267
relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 HG3    -0.088    2.788
relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F ALA 15 N      -0.094    3.344
relaxed_structure.pdb #5/C ARG 18 HH21  relaxed_structure.pdb #5/F PRO 18 HG2    -0.099    2.099
relaxed_structure.pdb #5/C ARG 18 CZ    relaxed_structure.pdb #5/F GLU 17 OE2    -0.103    3.283
relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 O      -0.106    2.586
relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 HB2    -0.106    2.586
relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 HA     -0.109    2.109
relaxed_structure.pdb #5/E SER 53 H     relaxed_structure.pdb #5/F GLU 9 OE2     -0.109    2.189
relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 HA     -0.113    2.593
relaxed_structure.pdb #5/C THR 14 HG1   relaxed_structure.pdb #5/F ALA 15 CB     -0.115    2.815
relaxed_structure.pdb #5/C PRO 58 CB    relaxed_structure.pdb #5/F ILE 11 HD13   -0.120    2.820
relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 C      -0.122    3.447
relaxed_structure.pdb #5/C ILE 11 HG13  relaxed_structure.pdb #5/F PRO 53 CB     -0.123    2.823
relaxed_structure.pdb #5/D LYS 109 NZ   relaxed_structure.pdb #5/F PRO 18 O      -0.123    2.828
relaxed_structure.pdb #5/C CYS 13 C     relaxed_structure.pdb #5/F ALA 15 HB3    -0.125    2.825
relaxed_structure.pdb #5/C ARG 18 NH1   relaxed_structure.pdb #5/F GLU 17 OE1    -0.132    2.837
relaxed_structure.pdb #5/C ILE 11 CG1   relaxed_structure.pdb #5/F PRO 53 CB     -0.134    3.534
relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F PRO 18 CG     -0.138    3.463
relaxed_structure.pdb #5/A ASP 34 OD2   relaxed_structure.pdb #5/F ARG 32 NH1    -0.139    2.844
relaxed_structure.pdb #5/C GLN 15 HG2   relaxed_structure.pdb #5/F SER 12 O      -0.148    2.628
relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F MET 54 CE     -0.150    3.350
relaxed_structure.pdb #5/C GLN 15 CG    relaxed_structure.pdb #5/F SER 12 O      -0.153    3.333
relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F ALA 7 O       -0.157    2.862
relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 HA     -0.159    2.784
relaxed_structure.pdb #5/C ILE 11 CD1   relaxed_structure.pdb #5/F PRO 53 CB     -0.177    3.577
relaxed_structure.pdb #5/C GLN 15 CG    relaxed_structure.pdb #5/F CYS 13 HA     -0.183    2.883
relaxed_structure.pdb #5/E ARG 43 NH2   relaxed_structure.pdb #5/F THR 8 CA      -0.185    3.510
relaxed_structure.pdb #5/C ALA 35 CA    relaxed_structure.pdb #5/F VAL 51 HA     -0.194    2.894
relaxed_structure.pdb #5/C GLN 15 HE21  relaxed_structure.pdb #5/F GLY 14 C      -0.195    2.895
relaxed_structure.pdb #5/D LYS 109 HG2  relaxed_structure.pdb #5/F GLU 19 OE1    -0.202    2.682
relaxed_structure.pdb #5/C ARG 18 NH1   relaxed_structure.pdb #5/F GLU 17 OE2    -0.203    2.908
relaxed_structure.pdb #5/E THR 54 O     relaxed_structure.pdb #5/F MET 54 CE     -0.206    3.386
relaxed_structure.pdb #5/C GLN 15 OE1   relaxed_structure.pdb #5/F SER 12 O      -0.206    3.166
relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F GLY 14 N      -0.207    3.532
relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 CA     -0.208    3.533
relaxed_structure.pdb #5/C PRO 58 HB2   relaxed_structure.pdb #5/F ILE 11 CD1    -0.211    2.911
relaxed_structure.pdb #5/E ARG 43 HH22  relaxed_structure.pdb #5/F ALA 7 C       -0.212    2.912
relaxed_structure.pdb #5/A THR 28 OG1   relaxed_structure.pdb #5/F ARG 32 NE     -0.215    2.940
relaxed_structure.pdb #5/C ILE 11 CD1   relaxed_structure.pdb #5/F MET 54 SD     -0.218    3.700
relaxed_structure.pdb #5/E THR 54 O     relaxed_structure.pdb #5/F MET 54 HE2    -0.218    2.698
relaxed_structure.pdb #5/C LYS 34 CB    relaxed_structure.pdb #5/F GLY 50 O      -0.221    3.401
relaxed_structure.pdb #5/A THR 28 HG1   relaxed_structure.pdb #5/F ARG 32 HH21   -0.224    2.224
relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 HB3    -0.227    2.227
relaxed_structure.pdb #5/E ARG 43 HH22  relaxed_structure.pdb #5/F THR 8 HA      -0.229    2.229
relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 CB     -0.230    3.410
relaxed_structure.pdb #5/E THR 54 CG2   relaxed_structure.pdb #5/F GLU 9 OE1     -0.230    3.410
relaxed_structure.pdb #5/E SER 53 CA    relaxed_structure.pdb #5/F GLU 9 OE2     -0.230    3.410
relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 CG     -0.231    3.631
relaxed_structure.pdb #5/C PRO 58 CG    relaxed_structure.pdb #5/F ILE 11 HD13   -0.233    2.933
relaxed_structure.pdb #5/C THR 14 HG1   relaxed_structure.pdb #5/F ALA 15 CA     -0.234    2.934
relaxed_structure.pdb #5/A ARG 27 NH1   relaxed_structure.pdb #5/F ASP 30 CG     -0.235    3.560
relaxed_structure.pdb #5/C PRO 58 HB3   relaxed_structure.pdb #5/F ILE 11 HD11   -0.242    2.242
relaxed_structure.pdb #5/C ALA 35 CA    relaxed_structure.pdb #5/F GLY 50 O      -0.243    3.423
relaxed_structure.pdb #5/C ALA 35 HB3   relaxed_structure.pdb #5/F VAL 51 HA     -0.244    2.244
relaxed_structure.pdb #5/A LYS 31 HZ1   relaxed_structure.pdb #5/F ASP 30 O      -0.246    2.326
relaxed_structure.pdb #5/C ILE 11 O     relaxed_structure.pdb #5/F PRO 53 CA     -0.247    3.427
relaxed_structure.pdb #5/C CYS 13 HB2   relaxed_structure.pdb #5/F PRO 53 HG3    -0.250    2.250
relaxed_structure.pdb #5/A THR 28 HB    relaxed_structure.pdb #5/F GLY 31 HA2    -0.251    2.251
relaxed_structure.pdb #5/C CYS 13 HB3   relaxed_structure.pdb #5/F PRO 53 CB     -0.254    2.954
relaxed_structure.pdb #5/A ARG 27 HH21  relaxed_structure.pdb #5/F ASP 30 CA     -0.255    2.955
relaxed_structure.pdb #5/C CYS 13 HB3   relaxed_structure.pdb #5/F PRO 53 HB2    -0.260    2.260
relaxed_structure.pdb #5/C PRO 58 HG3   relaxed_structure.pdb #5/F ILE 11 HD13   -0.265    2.265
relaxed_structure.pdb #5/A LYS 31 NZ    relaxed_structure.pdb #5/F ASP 30 O      -0.269    2.974
relaxed_structure.pdb #5/C PRO 58 HB2   relaxed_structure.pdb #5/F ILE 11 HD13   -0.269    2.269
relaxed_structure.pdb #5/C ALA 35 HA    relaxed_structure.pdb #5/F VAL 51 HA     -0.270    2.270
relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 C      -0.274    2.974
relaxed_structure.pdb #5/E ARG 43 HH21  relaxed_structure.pdb #5/F GLU 9 CD      -0.276    2.976
relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F GLY 14 H      -0.276    2.976
relaxed_structure.pdb #5/A ASP 34 CG    relaxed_structure.pdb #5/F ARG 32 HH22   -0.283    2.983
relaxed_structure.pdb #5/E THR 54 N     relaxed_structure.pdb #5/F GLU 9 OE2     -0.285    2.990
relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F GLY 14 H      -0.288    2.913
relaxed_structure.pdb #5/D LYS 109 HZ1  relaxed_structure.pdb #5/F PRO 18 C      -0.290    2.990
relaxed_structure.pdb #5/E ARG 43 CZ    relaxed_structure.pdb #5/F GLU 9 OE1     -0.291    3.471
relaxed_structure.pdb #5/C THR 14 HG22  relaxed_structure.pdb #5/F ALA 15 CB     -0.292    2.992
relaxed_structure.pdb #5/E THR 54 OG1   relaxed_structure.pdb #5/F MET 54 HE1    -0.299    2.799
relaxed_structure.pdb #5/E THR 54 CB    relaxed_structure.pdb #5/F GLU 9 OE2     -0.302    3.482
relaxed_structure.pdb #5/C CYS 13 HA    relaxed_structure.pdb #5/F PRO 53 HD3    -0.306    2.306
relaxed_structure.pdb #5/C ILE 11 CG1   relaxed_structure.pdb #5/F PRO 53 HB3    -0.311    3.011
relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F GLY 14 O      -0.312    3.017
relaxed_structure.pdb #5/A THR 28 HB    relaxed_structure.pdb #5/F GLY 31 C      -0.313    3.013
relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F GLU 17 CD     -0.314    3.639
relaxed_structure.pdb #5/A ARG 27 NH2   relaxed_structure.pdb #5/F ASP 30 CA     -0.317    3.642
relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 CB     -0.318    3.718
relaxed_structure.pdb #5/C ILE 11 HG13  relaxed_structure.pdb #5/F PRO 53 HB2    -0.319    2.319
relaxed_structure.pdb #5/C CYS 13 CB    relaxed_structure.pdb #5/F PRO 53 HB2    -0.326    3.026
relaxed_structure.pdb #5/E VAL 52 HG21  relaxed_structure.pdb #5/F ILE 11 CG2    -0.326    3.026
relaxed_structure.pdb #5/C CYS 13 O     relaxed_structure.pdb #5/F ALA 15 CB     -0.332    3.512
relaxed_structure.pdb #5/C GLN 15 NE2   relaxed_structure.pdb #5/F CYS 13 C      -0.336    3.661
relaxed_structure.pdb #5/D LYS 109 HZ2  relaxed_structure.pdb #5/F GLU 19 OE2    -0.338    2.418
relaxed_structure.pdb #5/C ALA 35 CB    relaxed_structure.pdb #5/F VAL 51 CA     -0.340    3.740
relaxed_structure.pdb #5/E SER 53 N     relaxed_structure.pdb #5/F GLU 9 OE2     -0.349    3.054
relaxed_structure.pdb #5/A THR 28 HB    relaxed_structure.pdb #5/F GLY 31 CA     -0.353    3.053
relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F PRO 18 HG2    -0.353    2.353
relaxed_structure.pdb #5/C ILE 11 HB    relaxed_structure.pdb #5/F PRO 53 O      -0.354    2.834
relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F MET 54 SD     -0.357    3.139
relaxed_structure.pdb #5/C PRO 58 HB3   relaxed_structure.pdb #5/F ILE 11 CD1    -0.364    3.064
relaxed_structure.pdb #5/C GLN 15 CD    relaxed_structure.pdb #5/F CYS 13 HA     -0.364    3.064
relaxed_structure.pdb #5/A LYS 31 NZ    relaxed_structure.pdb #5/F ASP 30 CG     -0.369    3.694
relaxed_structure.pdb #5/C THR 14 HG22  relaxed_structure.pdb #5/F ALA 15 HB3    -0.370    2.370
relaxed_structure.pdb #5/A THR 28 OG1   relaxed_structure.pdb #5/F ARG 32 CZ     -0.377    3.577
relaxed_structure.pdb #5/C ALA 35 N     relaxed_structure.pdb #5/F GLY 50 O      -0.377    3.082
relaxed_structure.pdb #5/C GLN 15 HE21  relaxed_structure.pdb #5/F GLY 14 CA     -0.381    3.081
relaxed_structure.pdb #5/C ARG 18 NH2   relaxed_structure.pdb #5/F PRO 18 CD     -0.381    3.706
relaxed_structure.pdb #5/C ARG 18 HH22  relaxed_structure.pdb #5/F PRO 18 CG     -0.386    3.086
relaxed_structure.pdb #5/C ILE 11 HD12  relaxed_structure.pdb #5/F PRO 53 CB     -0.388    3.088
relaxed_structure.pdb #5/E THR 54 HG22  relaxed_structure.pdb #5/F GLU 9 OE1     -0.396    2.876

160 contacts

color sel byhetero

select #5/A-F

28495 atoms, 28969 bonds, 160 pseudobonds, 1826 residues, 2 models selected

color sel byhetero

coulombic #5/A surfaces #5.1

Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum, -11.84, mean -0.24, maximum 17.92

coulombic #5/B surfaces #5.2

Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum, -13.17, mean 0.31, maximum 13.60

coulombic #5/C surfaces #5.3

Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum, -14.28, mean 0.87, maximum 12.27

coulombic #5/D surfaces #5.4

Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85, mean 2.10, maximum 15.14

coulombic #5/E surfaces #5.5

Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum, -10.97, mean 1.53, maximum 12.30

14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected

hide sel & #!1,5 atoms

select #5/A-E

27646 atoms, 28113 bonds, 1765 residues, 1 model selected

hide #5.1 models

hide #5.2 models

hide #5.3 models

hide #5.4 models

hide #5.5 models

hide #!2 models

ui tool show H-Bonds

hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	5 relaxed_structure.pdb

18 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH11  2.685  1.767
relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH21  2.667  1.732
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O    relaxed_structure.pdb #5/A LYS 31 HZ1   2.974  2.326
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2  relaxed_structure.pdb #5/A LYS 31 HZ2   2.680  1.727
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1  relaxed_structure.pdb #5/C ARG 18 HH11  2.837  1.944
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH11  2.908  2.025
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH22  2.733  1.757
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O    relaxed_structure.pdb #5/D LYS 109 HZ1  2.828  1.934
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1  relaxed_structure.pdb #5/D LYS 109 HZ2  2.673  1.723
relaxed_structure.pdb #5/E ARG 43 NE   relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HE    3.322  2.487
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O     relaxed_structure.pdb #5/E ARG 43 HH22  2.862  1.867
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HH21  2.749  1.745
relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E SER 53 H     3.054  2.189
relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E THR 54 HG1   2.662  1.709
relaxed_structure.pdb #5/F ARG 32 NE   relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HE    2.940  1.942
relaxed_structure.pdb #5/F ARG 32 NH1  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH12  2.844  1.934
relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HH21  3.342  2.567
relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH22  2.728  1.772

18 hydrogen bonds found

select #5/F:7,9,17-19,30,28,30,34

111 atoms, 106 bonds, 8 residues, 1 model selected

style sel stick

Changed 111 atom styles

select #5/F:28,34

30 atoms, 28 bonds, 2 residues, 1 model selected

style sel sphere

Changed 30 atom styles

select #5/F:32

24 atoms, 23 bonds, 1 residue, 1 model selected

style sel stick

Changed 24 atom styles

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54

167 atoms, 160 bonds, 9 residues, 1 model selected

style sel stick

Changed 167 atom styles

show sel atoms

hide #5.8 models

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 9 items

select #5/F:7,9,17-19,30,32

105 atoms, 101 bonds, 7 residues, 1 model selected

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 7 items

select :SF4

104 atoms, 156 bonds, 13 residues, 5 models selected

style sel & #3#!1 ball

Changed 40 atom styles

style sel & #3#!1 ball

Changed 40 atom styles

view front

[Repeated 1 time(s)]

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

view name hbond1

view front

view hbond1

view name hbond2

view name hbond3

view front

view back

view front

[Repeated 1 time(s)]

select #1/M:61@FE1

1 atom, 1 residue, 1 model selected

select #1/M:61@FE2

1 atom, 1 residue, 1 model selected

select #1/M:61@FE2#3/C:3003@FE2

2 atoms, 2 residues, 2 models selected

ui tool show Distances

distance style color #797979

[Repeated 2 time(s)]

distance style decimalPlaces 2

[Repeated 2 time(s)]

distance style radius 0.2

[Repeated 2 time(s)]

distance #1/M:61@FE2 #3/C:3003@FE2

Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE2: 11.23Å

~distance #1/M:61@FE2 #3/C:3003@FE2

select #1/M:61@FE2#3/C:3003@FE1

2 atoms, 2 residues, 2 models selected

distance #1/M:61@FE2 #3/C:3003@FE1

Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE1: 8.79Å

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

[Repeated 1 time(s)]

——— End of log from Thu Oct 3 09:47:21 2024 ———

opened ChimeraX session

view front

view back

view hBond1

Expected an objects specifier or a view name or a keyword

view hbond1

hide #6.1 models

view hbond2

view hbond3

view front

show #5.1 models

show #5.2 models

show #5.3 models

show #5.4 models

show #5.5 models

select add #5.5

1059 atoms, 66 residues, 1 model selected

select add #5.4

3336 atoms, 209 residues, 2 models selected

select add #5.3

4550 atoms, 289 residues, 3 models selected

select add #5.2

16065 atoms, 1022 residues, 4 models selected

select add #5.1

27646 atoms, 1765 residues, 5 models selected

transparency (#!5 & sel) 20

transparency (#!5 & sel) 30

graphics silhouettes false

graphics silhouettes true

show #!2 models

hide #!2 models

show #!2 models

select #2/F

1633 atoms, 1673 bonds, 9 pseudobonds, 164 residues, 2 models selected

hide sel atoms

hide sel cartoons

select #2/J

528 atoms, 546 bonds, 5 pseudobonds, 46 residues, 2 models selected

hide sel cartoons

hide sel atoms

select #2:BCR

1080 atoms, 1107 bonds, 27 residues, 1 model selected

select #2:BCR,LUT

1374 atoms, 1408 bonds, 34 residues, 1 model selected

color sel orange

color sel byhetero

show #5.6 models

coulombic #5/F surfaces #5.6

Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum, -13.89, mean -3.67, maximum 7.01

Nothing selected

select add #5.6

849 atoms, 61 residues, 1 model selected

transparency (#!5 & sel) 30

view front

hide #5.6 models

hide #5.5 models

hide #5.4 models

hide #5.3 models

hide #5.2 models

hide #5.1 models

show #5.1 models

show #5.2 models

show #5.3 models

show #5.4 models

show #5.5 models

hide #5.5 models

show #5.5 models

hide #5.5 models

show #5.5 models

show #5.6 models

help help:user

view name front

turn x 180

view front

turn y 180

hide #5.3 models

hide #5.4 models

hide #5.5 models

hide #5.6 models

show #5.3 models

show #5.4 models

show #5.5 models

show #5.6 models

hide #5.5 models

hide #5.4 models

hide #5.3 models

show #5.4 models

show #5.5 models

hide #5.4 models

hide #5.5 models

show #5.4 models

hide #5.4 models

turn y 180

[Repeated 1 time(s)]

view name back

view front

view back

select #2/I/H/L

2569 atoms, 2652 bonds, 18 pseudobonds, 292 residues, 2 models selected

hide sel cartoons

hide sel atoms

hide #5.6 models

view name back

show #5.6 models

show #5.4 models

hide #5.4 models

hide #5.6 models

view name back

view front

view back

view front

show #5.3 models

show #5.4 models

show #5.5 models

hide #5.5 models

hide #5.4 models

hide #5.3 models

show #5.3 models

show #5.4 models

show #5.5 models

show #5.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

——— End of log from Thu Oct 3 21:28:49 2024 ———

opened ChimeraX session

view front

view backZoom

Expected an objects specifier or a view name or a keyword

view hbond2

view back

hide #5.6 models

show #5.6 models

show #!4 models

hide #!5 models

show #!5 models

hide #!4 models

hide #5.6 models

show #5.6 models

hide #5.6 models

show #5.6 models

view front

hide #5.6 models

hide #!1 models

show #!18 models

rename #6 id #8

2569 atoms, 2652 bonds, 19 pseudobonds, 292 residues, 4 models selected

hide #5.5 models

hide #5.4 models

hide #5.3 models

show #!1 models

show #8.1 models

rename #1 id #6

rename #2 id #1

rename #3 id #2

rename #4 id #3

rename #18 id #4

hide #!4 models

ui tool show Matchmaker

matchmaker #!6 to #5/B pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain B (#5) with 2fdn, chain M (#6), sequence alignment score = 4
Fewer than 3 residues aligned; cannot match relaxed_structure.pdb, chain B with 2fdn, chain M

ui tool show Matchmaker

matchmaker #!6 to #5/F pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 170.3
RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs: 2.909)

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

select #5@@draw_mode=0

28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected

hide #5.1 models

hide #5.7 models

28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 8 models selected

select subtract #5.6

27425 atoms, 27831 bonds, 1756 residues, 7 models selected

select subtract #5.5

26415 atoms, 26811 bonds, 1693 residues, 6 models selected

select subtract #5.4

24160 atoms, 24526 bonds, 1551 residues, 5 models selected

select subtract #5.3

23024 atoms, 23432 bonds, 1472 residues, 4 models selected

select subtract #5.2

11509 atoms, 11705 bonds, 739 residues, 3 models selected

select subtract #5.1

1 model selected

hide #5.2 models

select #5/A-F@@draw_mode=0

28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected

Nothing selected

hide #!5 models

show #!5 models

select #5/F:1-55@@draw_mode=0

600 atoms, 555 bonds, 48 residues, 1 model selected

select #5 &protein &@@draw_mode=0

28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected

select #5/C:1-100 &@@draw_mode=0

1136 atoms, 1094 bonds, 79 residues, 1 model selected

select #5/C:1-100@@draw_mode=0

1136 atoms, 1094 bonds, 79 residues, 1 model selected

select subtract #5.3

1 model selected

select #5/C:1-100@@draw_mode=0

1136 atoms, 1094 bonds, 79 residues, 1 model selected

select #5/C:11,14-15,34-35/E:52/F:8,52-54

154 atoms, 149 bonds, 17 pseudobonds, 10 residues, 2 models selected

select #5/C:11,14-15,34-35/E:52/F:8,51-54

170 atoms, 165 bonds, 22 pseudobonds, 11 residues, 2 models selected

select #5/C:11,14-15,34-35/E:52/F:8,51,53,54

159 atoms, 153 bonds, 22 pseudobonds, 10 residues, 2 models selected

select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54

169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected

169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 5 models selected

select subtract #5.6

98 atoms, 94 bonds, 6 residues, 4 models selected

select subtract #5.5

82 atoms, 79 bonds, 5 residues, 3 models selected

select subtract #5.3

1 model selected

select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54

169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

hide sel atoms

select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54

202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected

hide sel atoms

show sel atoms

14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected

hide sel & #!5-6 atoms

style sel & #!5-6 stick

Changed 14343 atom styles

select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54

202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected

style sel stick

Changed 202 atom styles

select #5/F:Cys

88 atoms, 80 bonds, 8 residues, 1 model selected

select #5/F:Cys|#6:Cys

168 atoms, 152 bonds, 16 residues, 2 models selected

ui tool show Matchmaker

matchmaker #!6 & sel to #5/B & sel pairing bs

No 'to' chains specified

ui tool show Matchmaker

matchmaker #!6 & sel to #5/F & sel pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)

select #6:Cys

80 atoms, 72 bonds, 8 residues, 1 model selected

show sel atoms

select #5:11-14

355 atoms, 352 bonds, 24 residues, 1 model selected

show sel atoms

style sel stick

Changed 355 atom styles

hide #!6 models

14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected

hide (#!5 & sel) target a

show #!6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

——— End of log from Fri Oct 4 09:37:44 2024 ———

opened ChimeraX session

select #5/F:13

11 atoms, 10 bonds, 1 residue, 1 model selected

ui tool show Rotamers

swapaa interactive sel CYH rotLib Dunbrack

relaxed_structure.pdb #5/F CYS 13: phi -84.1, psi 65.7 trans
Changed 9 bond radii

swapaa #!5/F:13 CYH criteria 2 rotLib Dunbrack

Using Dunbrack library
relaxed_structure.pdb #!5/F CYS 13: phi -84.1, psi 65.7 trans
Applying CYS rotamer (chi angles: -178.7) to relaxed_structure.pdb #!5/F CYS 13

select #6:Cys

80 atoms, 72 bonds, 8 residues, 1 model selected

hide sel atoms

view front

hide #!6 models

show #!6 models

select #5/F:Cys|#6:Cys

165 atoms, 149 bonds, 16 residues, 2 models selected

ui tool show Matchmaker

matchmaker #!6 & sel to #5/F & sel pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)

view front

matchmaker #!6 & sel to #5/F & sel pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)

view front

matchmaker #!6 & sel to #5/F & sel pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)

view name front

turn y 180

view front

turn y 180

turn x 30

show #5.1 models

show #5.2 models

show #5.3 models

show #5.4 models

show #5.5 models

hide #5.5 models

show #5.5 models

show #5.6 models

hide #5.3 models

hide #5.4 models

coulombic #5/F surfaces #5.6

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum, -13.91, mean -3.63, maximum 7.03

show #5.3 models

show #5.4 models

hide #5.4 models

hide #5.3 models

transparency (#!5-6 & sel) 30

select add #5.6

844 atoms, 61 residues, 1 model selected

transparency (#!5 & sel) 30

view name back

help help:user

Named views: back, front, hbond1, hbond2, hbond3

view delete hbond1 hbond2 hbond3

Expected fewer arguments

Named views: back, front, hbond1, hbond2, hbond3

help help:user

view delete hbond1

view delete hbond2

view delete hbond3

Named views: back, front

view front

hide #5.5 models

hide #5.6 models

view back

show #5.8 models

select add #5.8

160 pseudobonds, 1 model selected

160 pseudobonds, 1 model selected

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

——— End of log from Fri Oct 4 10:09:32 2024 ———

opened ChimeraX session

select #5/A-E

27646 atoms, 28113 bonds, 1765 residues, 1 model selected

select #5/A-E &~H

13989 atoms, 14456 bonds, 1765 residues, 1 model selected

ui tool show Contacts

contacts sel setAttrs true restrict "#5/F &~H" resSeparation 5 interModel false intraMol false select true color #76d6ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

66 contacts
                atom1                                  atom2                  overlap  distance
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 CD    0.340    2.985
relaxed_structure.pdb #5/C PRO 58 CB   relaxed_structure.pdb #5/F ILE 11 CD1   0.169    3.231
relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F GLY 14 N     0.152    3.098
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 CD    0.062    3.263
relaxed_structure.pdb #5/A ARG 27 CZ   relaxed_structure.pdb #5/F ASP 30 OD1   0.055    3.125
relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1   0.038    2.667
relaxed_structure.pdb #5/C GLN 15 CD   relaxed_structure.pdb #5/F SER 12 O     0.034    3.146
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1   0.032    2.673
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2   0.025    2.680
relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1   0.020    2.685
relaxed_structure.pdb #5/C LYS 34 C    relaxed_structure.pdb #5/F GLY 50 O     0.019    3.161
relaxed_structure.pdb #5/C PRO 58 CG   relaxed_structure.pdb #5/F ILE 11 CD1   0.015    3.385
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE2   0.011    2.694
relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 CD     -0.001    3.201
relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 NH2   -0.023    2.728
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2   -0.028    2.733
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1    -0.044    2.749
relaxed_structure.pdb #5/C ARG 18 CZ   relaxed_structure.pdb #5/F GLY 14 O     -0.062    3.242
relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 CG    -0.076    3.401
relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 CZ    -0.080    3.260
relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2    -0.082    2.662
relaxed_structure.pdb #5/E SER 53 C    relaxed_structure.pdb #5/F GLU 9 OE2    -0.087    3.267
relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F ALA 15 N     -0.094    3.344
relaxed_structure.pdb #5/C ARG 18 CZ   relaxed_structure.pdb #5/F GLU 17 OE2   -0.103    3.283
relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F GLY 14 C     -0.122    3.447
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O     -0.123    2.828
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1   -0.132    2.837
relaxed_structure.pdb #5/C ILE 11 CG1  relaxed_structure.pdb #5/F PRO 53 CB    -0.134    3.534
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F PRO 18 CG    -0.138    3.463
relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 NH1   -0.139    2.844
relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F MET 54 CE    -0.150    3.350
relaxed_structure.pdb #5/C GLN 15 CG   relaxed_structure.pdb #5/F SER 12 O     -0.153    3.333
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O      -0.157    2.862
relaxed_structure.pdb #5/C ILE 11 CD1  relaxed_structure.pdb #5/F PRO 53 CB    -0.177    3.577
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F THR 8 CA     -0.185    3.510
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2   -0.203    2.908
relaxed_structure.pdb #5/E THR 54 O    relaxed_structure.pdb #5/F MET 54 CE    -0.206    3.386
relaxed_structure.pdb #5/C GLN 15 OE1  relaxed_structure.pdb #5/F SER 12 O     -0.206    3.166
relaxed_structure.pdb #5/C GLN 15 CD   relaxed_structure.pdb #5/F GLY 14 N     -0.207    3.532
relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F GLY 14 CA    -0.208    3.533
relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 NE    -0.215    2.940
relaxed_structure.pdb #5/C ILE 11 CD1  relaxed_structure.pdb #5/F MET 54 SD    -0.218    3.700
relaxed_structure.pdb #5/C LYS 34 CB   relaxed_structure.pdb #5/F GLY 50 O     -0.221    3.401
relaxed_structure.pdb #5/C ILE 11 O    relaxed_structure.pdb #5/F PRO 53 CB    -0.230    3.410
relaxed_structure.pdb #5/E THR 54 CG2  relaxed_structure.pdb #5/F GLU 9 OE1    -0.230    3.410
relaxed_structure.pdb #5/E SER 53 CA   relaxed_structure.pdb #5/F GLU 9 OE2    -0.230    3.410
relaxed_structure.pdb #5/C CYS 13 CB   relaxed_structure.pdb #5/F PRO 53 CG    -0.231    3.631
relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 CG    -0.235    3.560
relaxed_structure.pdb #5/C ALA 35 CA   relaxed_structure.pdb #5/F GLY 50 O     -0.243    3.423
relaxed_structure.pdb #5/C ILE 11 O    relaxed_structure.pdb #5/F PRO 53 CA    -0.247    3.427
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O     -0.269    2.974
relaxed_structure.pdb #5/E THR 54 N    relaxed_structure.pdb #5/F GLU 9 OE2    -0.285    2.990
relaxed_structure.pdb #5/E ARG 43 CZ   relaxed_structure.pdb #5/F GLU 9 OE1    -0.291    3.471
relaxed_structure.pdb #5/E THR 54 CB   relaxed_structure.pdb #5/F GLU 9 OE2    -0.302    3.482
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLY 14 O     -0.312    3.017
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 CD    -0.314    3.639
relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 CA    -0.317    3.642
relaxed_structure.pdb #5/C CYS 13 CB   relaxed_structure.pdb #5/F PRO 53 CB    -0.318    3.718
relaxed_structure.pdb #5/C CYS 13 O    relaxed_structure.pdb #5/F ALA 15 CB    -0.332    3.512
relaxed_structure.pdb #5/C GLN 15 NE2  relaxed_structure.pdb #5/F CYS 13 C     -0.336    3.661
relaxed_structure.pdb #5/C ALA 35 CB   relaxed_structure.pdb #5/F VAL 51 CA    -0.340    3.740
relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2    -0.349    3.054
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 CG    -0.369    3.694
relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 CZ    -0.377    3.577
relaxed_structure.pdb #5/C ALA 35 N    relaxed_structure.pdb #5/F GLY 50 O     -0.377    3.082
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F PRO 18 CD    -0.381    3.706

66 contacts

style sel sphere

Changed 75 atom styles

name frozen contacts sel

select contacts

16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected

help help:user

help help:user/selectcontacts.html

[Repeated 1 time(s)]

interfaces select #5/A & ::polymer_type>0 contacting #5/F & ::polymer_type>0 areaCutoff 0

4 contacting residues

select contacts

16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected

style sel stick

Changed 16975 atom styles

hide #5.8 models

select subtract #5.8

16975 atoms, 38 bonds, 1093 residues, 6 models selected

close #5.8

hide #5.9 models

show #5.9 models

close #5.9

close #5.7

ui tool show H-Bonds

select #5/A-E

27646 atoms, 28113 bonds, 1765 residues, 1 model selected

hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	5 relaxed_structure.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH11  2.685  1.767
relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH21  2.667  1.732
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O    relaxed_structure.pdb #5/A LYS 31 HZ1   2.974  2.326
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2  relaxed_structure.pdb #5/A LYS 31 HZ2   2.680  1.727
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1  relaxed_structure.pdb #5/C ARG 18 HH11  2.837  1.944
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH11  2.908  2.025
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH22  2.733  1.757
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O    relaxed_structure.pdb #5/D LYS 109 HZ1  2.828  1.934
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1  relaxed_structure.pdb #5/D LYS 109 HZ2  2.673  1.723
relaxed_structure.pdb #5/E ARG 43 NE   relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HE    3.322  2.487
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O     relaxed_structure.pdb #5/E ARG 43 HH22  2.862  1.867
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HH21  2.749  1.745
relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E SER 53 H     3.054  2.189
relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E THR 54 HG1   2.662  1.709
relaxed_structure.pdb #5/F CYS 13 SG   relaxed_structure.pdb #5/C CYS 13 O    no hydrogen                             3.816  N/A
relaxed_structure.pdb #5/F ARG 32 NE   relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HE    2.940  1.942
relaxed_structure.pdb #5/F ARG 32 NH1  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH12  2.844  1.934
relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HH21  3.342  2.567
relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH22  2.728  1.772

19 hydrogen bonds found

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32

272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected

14612 atoms, 1922 residues, 3 models selected

hide sel & #!5-6 atoms

select #5/A-E

27646 atoms, 28113 bonds, 1765 residues, 1 model selected

hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	5 relaxed_structure.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
relaxed_structure.pdb #5/A ARG 27 NH1  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH11  2.685  1.767
relaxed_structure.pdb #5/A ARG 27 NH2  relaxed_structure.pdb #5/F ASP 30 OD1  relaxed_structure.pdb #5/A ARG 27 HH21  2.667  1.732
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 O    relaxed_structure.pdb #5/A LYS 31 HZ1   2.974  2.326
relaxed_structure.pdb #5/A LYS 31 NZ   relaxed_structure.pdb #5/F ASP 30 OD2  relaxed_structure.pdb #5/A LYS 31 HZ2   2.680  1.727
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE1  relaxed_structure.pdb #5/C ARG 18 HH11  2.837  1.944
relaxed_structure.pdb #5/C ARG 18 NH1  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH11  2.908  2.025
relaxed_structure.pdb #5/C ARG 18 NH2  relaxed_structure.pdb #5/F GLU 17 OE2  relaxed_structure.pdb #5/C ARG 18 HH22  2.733  1.757
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F PRO 18 O    relaxed_structure.pdb #5/D LYS 109 HZ1  2.828  1.934
relaxed_structure.pdb #5/D LYS 109 NZ  relaxed_structure.pdb #5/F GLU 19 OE1  relaxed_structure.pdb #5/D LYS 109 HZ2  2.673  1.723
relaxed_structure.pdb #5/E ARG 43 NE   relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HE    3.322  2.487
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F ALA 7 O     relaxed_structure.pdb #5/E ARG 43 HH22  2.862  1.867
relaxed_structure.pdb #5/E ARG 43 NH2  relaxed_structure.pdb #5/F GLU 9 OE1   relaxed_structure.pdb #5/E ARG 43 HH21  2.749  1.745
relaxed_structure.pdb #5/E SER 53 N    relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E SER 53 H     3.054  2.189
relaxed_structure.pdb #5/E THR 54 OG1  relaxed_structure.pdb #5/F GLU 9 OE2   relaxed_structure.pdb #5/E THR 54 HG1   2.662  1.709
relaxed_structure.pdb #5/F CYS 13 SG   relaxed_structure.pdb #5/C CYS 13 O    no hydrogen                             3.816  N/A
relaxed_structure.pdb #5/F ARG 32 NE   relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HE    2.940  1.942
relaxed_structure.pdb #5/F ARG 32 NH1  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH12  2.844  1.934
relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A THR 28 OG1  relaxed_structure.pdb #5/F ARG 32 HH21  3.342  2.567
relaxed_structure.pdb #5/F ARG 32 NH2  relaxed_structure.pdb #5/A ASP 34 OD2  relaxed_structure.pdb #5/F ARG 32 HH22  2.728  1.772

19 hydrogen bonds found

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32

272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected

style sel ball

Changed 272 atom styles

style sel stick

Changed 272 atom styles

name frozen hBonds sel

[Repeated 1 time(s)]

help help:user

name delete all

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32

272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected

name frozen Hbonds sel

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

view front

interfaces select #5/A & ::polymer_type>0 contacting #5/F & ::polymer_type>0 areaCutoff 0

4 contacting residues

hide #5.1 models

hide #5.2 models

interfaces select #5/B & ::polymer_type>0 contacting #5/F & ::polymer_type>0 areaCutoff 0

0 contacting residues

interfaces select #5/C & ::polymer_type>0 contacting #5/F & ::polymer_type>0 areaCutoff 0

9 contacting residues

help help:user

info residues sel

residue id #5/C:11 name ILE index 10
residue id #5/C:13 name CYS index 12
residue id #5/C:14 name THR index 13
residue id #5/C:15 name GLN index 14
residue id #5/C:18 name ARG index 17
residue id #5/C:34 name LYS index 33
residue id #5/C:35 name ALA index 34
residue id #5/C:37 name GLN index 36
residue id #5/C:58 name PRO index 57

interfaces select #5/C#5/F & ::polymer_type>0 contacting #1/1 & ::polymer_type>0 areaCutoff 0

0 contacting residues

interfaces select #5/F & ::polymer_type>0 contacting #5/C & ::polymer_type>0 areaCutoff 0

10 contacting residues

interfaces select #5/F & ::polymer_type>0 contacting #5/A#5/B#5/C#5/D & ::polymer_type>0 areaCutoff 0

15 contacting residues

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

info residues sel

residue id #5/F:11 name ILE index 10
residue id #5/F:12 name SER index 11
residue id #5/F:13 name CYS index 12
residue id #5/F:14 name GLY index 13
residue id #5/F:15 name ALA index 14
residue id #5/F:17 name GLU index 16
residue id #5/F:18 name PRO index 17
residue id #5/F:19 name GLU index 18
residue id #5/F:30 name ASP index 29
residue id #5/F:31 name GLY index 30
residue id #5/F:32 name ARG index 31
residue id #5/F:50 name GLY index 49
residue id #5/F:51 name VAL index 50
residue id #5/F:53 name PRO index 52
residue id #5/F:54 name MET index 53

select #5/F:11-15,19,29,31,49,50,52,53

131 atoms, 126 bonds, 12 residues, 1 model selected

select #5/F:11-15,29,31,49,50,52,53

116 atoms, 112 bonds, 11 residues, 1 model selected

select #5/F:11-15,29,31,49,50,52,53

116 atoms, 112 bonds, 11 residues, 1 model selected

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 11 items

select #5/F:11-15,29,31,49,50,52,53

116 atoms, 112 bonds, 11 residues, 1 model selected

name frozen buriedFchain sel

style sel sphere

Changed 116 atom styles

interfaces select #5/A#5/B#5/C#5/D#5/E & ::polymer_type>0 contacting #5/F & ::polymer_type>0 areaCutoff 0

20 contacting residues

info residues sel

residue id #5/A:27 name ARG index 26
residue id #5/A:28 name THR index 27
residue id #5/A:31 name LYS index 30
residue id #5/A:34 name ASP index 33
residue id #5/C:11 name ILE index 10
residue id #5/C:13 name CYS index 12
residue id #5/C:14 name THR index 13
residue id #5/C:15 name GLN index 14
residue id #5/C:18 name ARG index 17
residue id #5/C:34 name LYS index 33
residue id #5/C:35 name ALA index 34
residue id #5/C:37 name GLN index 36
residue id #5/C:58 name PRO index 57
residue id #5/D:109 name LYS index 108
residue id #5/E:41 name VAL index 40
residue id #5/E:43 name ARG index 42
residue id #5/E:51 name ASN index 50
residue id #5/E:52 name VAL index 51
residue id #5/E:54 name THR index 53
residue id #5/E:56 name ASN index 55

select #5/C:11,13-15,34-37,58/E:41,51-52,56

206 atoms, 200 bonds, 13 residues, 1 model selected

show sel atoms

style sel sphere

Changed 206 atom styles

14612 atoms, 1922 residues, 3 models selected

hide sel & #!5-6 atoms

select #5/C:11,13-15,34-37,58/E:41,51-52,56

206 atoms, 200 bonds, 13 residues, 1 model selected

name frozen buriedA_Echain sel

select buriedA_Echain|buriedFChain

Expected an objects specifier or a keyword

select buriedA_Echain | buriedFChain

Expected a keyword

select buriedA_Echain

2273 atoms, 200 bonds, 146 residues, 1 model selected

select buriedA_Echain | buriedFchain

3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected

select buriedA_Echain

2273 atoms, 200 bonds, 146 residues, 1 model selected

select buriedA_Echain | buriedFchain

3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected

select Hbonds

16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected

show sel atoms

hide sel atoms

select buriedA_Echain | buriedFchain

3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected

name frozen A_EinterfaceF sel

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32

272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected

show sel atoms

select #5/C:Cys/F:Cys &~H &~/C:33

96 atoms, 157 bonds, 1 pseudobond, 16 residues, 2 models selected

show sel atoms

select buriedA_Echain | buriedFchain

3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected

select buriedA_Echain

2273 atoms, 200 bonds, 146 residues, 1 model selected

select #5/C:11,13-15,34-37,58/E:41,51-52,56

206 atoms, 200 bonds, 13 residues, 1 model selected

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53

322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H

162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected

show sel atoms

view front

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

name delete all

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H

162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected

name frozen interfaceNoHB sel

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32

272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected

name frozen interfaceHB sel

select interfaceHB

16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected

style sel ball

Changed 16975 atom styles

style sel sphere

Changed 16975 atom styles

select interfaceHB

16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected

style sel stick

Changed 16975 atom styles

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H

162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected

style sel sphere

Changed 162 atom styles

view front

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

show #5.1 models

show #5.2 models

show #5.3 models

show #5.4 models

show #5.5 models

show #5.6 models

view front

hide #8.1 models

ui tool show "Color Key"

ui mousemode right "color key"

key blue-white-red :min : :+

key blue-white-red :min :0 :+

key blue-white-red :+ :0 :+

key blue-white-red :+ :0 :-

key bold true

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key fontSize 16

key ticks true

key tickLength 8.0

key tickThickness 3.0

key tickLength 6.0

key tickLength 4.0

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key tickLength 0.0

key tickLength 2.0

key tickLength 4.0

key size 0.25000,0.04000

key size 0.25000,0.03000

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ui mousemode right translate

hide #7 models

show #7 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

hide #5.6 models

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32

272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H

162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected

transparency (#!5 & sel) 80

transparency (#!5 & sel) 100

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53

322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected

transparency (#!5 & sel) 100

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53

322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected

transparency (#!5 & sel) 90

transparency (#!5 & sel) 70

transparency (#!5 & sel) 100

hide #5.5 models

show #5.5 models

hide #5.5 models

show #5.5 models

hide #5.5 models

show #5.5 models

hide #5.5 models

show #5.6 models

hide #5.6 models

show #5.5 models

select add #5.6

844 atoms, 61 residues, 1 model selected

select add #5.5

1903 atoms, 127 residues, 2 models selected

select add #5.4

4180 atoms, 270 residues, 3 models selected

select add #5.3

5394 atoms, 350 residues, 4 models selected

select add #5.2

16909 atoms, 1083 residues, 5 models selected

select add #5.1

28490 atoms, 1826 residues, 6 models selected

show #5.6 models

transparency (#!5 & sel) 30

select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53

322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected

style sel stick

Changed 322 atom styles

view front

hide #5.6 models

show #5.6 models

hide #5.6 models

show #5.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt All surfaces front .png" width 1508 height 1200 supersample 3 transparentBackground true

hide #5.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt no F surface front .png" width 1508 height 1200 supersample 3 transparentBackground true

show #5.6 models

hide #5.5 models

hide #5.4 models

hide #5.3 models

view back

show #5.3 models

hide #5.3 models

show #5.5 models

hide #5.5 models

trurn y 90

Unknown command: trurn y 90

turn y 90

show #5.3 models

turn y 30

view back

[Repeated 1 time(s)]

turn y 30

[Repeated 1 time(s)]

turn y 10

turn x 10

[Repeated 1 time(s)]

turn y -10

[Repeated 1 time(s)]

view back

turn x 10

turn y 30

[Repeated 1 time(s)]

turn x 10

view back

turn x 60

turn y 60

turn y -30

view back

turn x 10

turn y 40

turn y 10

turn x 10

view back

turn y 50

turn x 20

show #5.4 models

show #5.5 models

view name side

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

hide #5.6 models

hide #5.5 models

hide #5.4 models

hide #5.3 models

show #5.5 models

hide #5.5 models

show #5.5 models

show #5.6 models

show #5.4 models

show #5.3 models

view front

view side

view front

hide #5.5 models

show #5.5 models

view side

view front

hide #5.6 models

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54

167 atoms, 160 bonds, 9 residues, 1 model selected

transparency (#!5 & sel) 80

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54

167 atoms, 160 bonds, 9 residues, 1 model selected

transparency (#!5 & sel) 90

turn x 10

turn x -10

turn x 5

turn x -5

view side

view front

[Repeated 1 time(s)]

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

turn x 5

turn y 5

turn x 5

[Repeated 1 time(s)]

turn y -5

view front

turn x 15

show #5.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

select add #5.6

844 atoms, 61 residues, 1 model selected

select add #5.5

1903 atoms, 127 residues, 2 models selected

select add #5.4

4180 atoms, 270 residues, 3 models selected

select add #5.3

5394 atoms, 350 residues, 4 models selected

select add #5.2

16909 atoms, 1083 residues, 5 models selected

select add #5.1

28490 atoms, 1826 residues, 6 models selected

transparency (#!5 & sel) 20

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

hide #5.7 models

show #5.7 models

hide #5.6 models

show #5.6 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

view name front

turn y 50

hide #5.4 models

show #5.4 models

hide #5.5 models

show #5.5 models

view front

view side

hide #5.5 models

show #5.5 models

hide #5.4 models

show #5.4 models

view front

turn y 60

hide #5.4 models

show #5.4 models

view side

hide #5.4 models

view front

turn y 60

turn y -60

[Repeated 1 time(s)]

show #5.4 models

view front

hide #5.5 models

show #5.5 models

view side

view front

view side

view front

turn y 90

hide #5.6 models

show #5.6 models

hide #5.6 models

show #5.6 models

hide #5.6 models

show #5.6 models

view front

turn x 90

hide #5.6 models

show #5.6 models

view front

turn 30

Expected an axis vector or a keyword

turn y 30

hide #5.6 models

show #5.6 models

hide #5.4 models

show #5.4 models

hide #5.5 models

show #5.5 models

turn y -30

[Repeated 3 time(s)]

turn x 30

turn x 10

turn x 5

view front

turn x 45

turn x -45

turn y 30

view front

turn y 30

view front

turn y -30

turn x -45

turn x 45

[Repeated 1 time(s)]

view front

turn y -45

view front

turn y -45

turn x 45

view front

turn y -50

turn x -45

view front

turn y -50

turn x 45

turn x -15

view front

turn y -50

turn x 30

view front

turn y -60

view front

[Repeated 1 time(s)]

help help:user

trun 1,1,0 45

Unknown command: trun 1,1,0 45

turn 1,1,0 45

turn 1,1,0 -45

turn -1,1,0 45

view front

turn -1,1,0 -45

turn y 60

turn y -60

[Repeated 1 time(s)]

view front

view back

view front

turn y 180

turn x 45

hide #5.4 models

show #5.4 models

view front

turn y 180

turn x 45

[Repeated 1 time(s)]

turn x 15

view front

turn y 180

turn x 60

view front

turn y 180

turn x 60

turn x 30

view front

turn x 90

hide #5.6 models

show #5.6 models

view front

turn x 60

view front

[Repeated 1 time(s)]

turn y 180

turn x 90

turn x 30

view front

turn y 180

turn x 120

view front

turn y 190

turn x 130

turn y 10

[Repeated 2 time(s)]

view front

turn y 200

turn x 145

view front

turn x 145

turn y 200

view front

view name side

view front

hide #5.6 models

1 pseudobond, 2 models selected

Nothing selected

1 pseudobond, 2 models selected

Nothing selected

1 pseudobond, 2 models selected

Nothing selected

1 pseudobond, 2 models selected

Nothing selected

1 pseudobond, 2 models selected

Nothing selected

show #8.1 models

hide #8.1 models

select #5/A:27,28,31,34/C:18/D:109/E:43,53,54

167 atoms, 160 bonds, 9 residues, 1 model selected

transparency (#!5 & sel) 90

hide #7 models

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

view name HbondsZoom

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

view HbondsZoom

select #5/C:11,13-15,34-37,58

146 atoms, 143 bonds, 9 residues, 1 model selected

select #5/C:11,13-15

61 atoms, 59 bonds, 4 residues, 1 model selected

select #5/C:13-15

42 atoms, 41 bonds, 3 residues, 1 model selected

transparency (#!5 & sel) 90

view HbondsZoom

select #5/C:13-15

42 atoms, 41 bonds, 3 residues, 1 model selected

transparency (#!5 & sel) 20

select #5/C:11

19 atoms, 18 bonds, 1 residue, 1 model selected

transparency (#!5 & sel) 90

graphics silhouettes false

graphics silhouettes true

view name HbondsZoom

view front

view side

view HbondsZoom

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

——— End of log from Fri Oct 4 15:14:28 2024 ———

opened ChimeraX session

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3 transparentBackground true

hide #!8 models

show #!8 models

select #6:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

select #3/B:1

5 atoms, 4 bonds, 1 residue, 1 model selected

select #3/B:1-2

17 atoms, 17 bonds, 2 residues, 1 model selected

select #6:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

select #3/B:1-2

17 atoms, 17 bonds, 2 residues, 1 model selected

select #6:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

select #6:1-2,8-24,30-47#5/F:1-2

480 atoms, 481 bonds, 39 residues, 2 models selected

select #6:1-2,8-24,30-47#5/F:1-2,8-24

695 atoms, 697 bonds, 56 residues, 2 models selected

ui tool show Matchmaker

matchmaker #!6 to #5/F pairing bs showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 170.3
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: relaxed_structure.pdb #5/F, 2fdn #6/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs: 2.909)

sequence header 1 consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 1

select #6:1-2,8-24,30-47#5/F:1-2,10-26

696 atoms, 698 bonds, 56 residues, 2 models selected

select #6:1-2,8-24,30-47#5/F:1-2,10-26,35-52

925 atoms, 927 bonds, 74 residues, 2 models selected

show sel cartoons

select #5

28492 atoms, 28966 bonds, 19 pseudobonds, 1826 residues, 2 models selected

hide sel cartoons

show sel cartoons

select #6

762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected

hide sel cartoons

select #5/F:1-2,10-26,35-52

478 atoms, 479 bonds, 37 residues, 1 model selected

color (#!5 & sel) orange

color sel byhetero

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3 transparentBackground true

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3 transparentBackground true

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"

——— End of log from Sun Oct 6 13:38:31 2024 ———

opened ChimeraX session

hide #!1 models

close #20

close #8

close #7

hide #5.5 models

hide #5.3 models

hide #5.2 models

hide #5.1 models

hide #5.4 models

hide #2 models

show #2 models

select #2

24 atoms, 36 bonds, 3 residues, 1 model selected

select #2 :<3 &#5/A-C:Cys

132 atoms, 120 bonds, 12 residues, 1 model selected

show sel atoms

color sel byhetero

select #2 :<3 &#5/A-C:Cys &H

60 atoms, 12 residues, 1 model selected

hide sel atoms

select #2 :<3 &#5/A-C:Cys

132 atoms, 120 bonds, 12 residues, 1 model selected

style sel stick

Changed 132 atom styles

show #!1 models

hide #2 models

hide #!5 models

hide #!1 models

show #!1 models

select #1/B:549

8 atoms, 7 bonds, 1 residue, 1 model selected

show sel cartoons

show #!5 models

hide #!5 models

select #1/A-B

18021 atoms, 18789 bonds, 361 pseudobonds, 1592 residues, 2 models selected

show sel cartoons

show #!5 models

hide #!1 models

hide #!5 models

show #!1 models

show #2 models

hide #2 models

show #2 models

hide #2 models

show #2 models

hide #2 models

show #2 models

hide #2 models

close #1

show #2 models

close #3-4

show #!5 models

ui mousemode right "translate selected atoms"

ui mousemode right "translate selected models"

rename #2 "PSI Fx Fa Fb clusters"

rename #5 id #1

rename #6 id #3

rename #1 "relaxed PsaABCDE BFd(F) complex"

show #1.1 models

show #1.2 models

show #1.3 models

show #1.4 models

show #1.5 models

show #1.6 models

hide #1.5 models

hide #1.4 models

hide #1.3 models

hide #1.2 models

hide #1.1 models

hide #1.6 models

rename #5/F

No name or id option specified for renaming

select #5/F

Nothing selected

select #1/F

846 atoms, 853 bonds, 61 residues, 1 model selected

color sel bychain

color sel byhetero

help help:user

color #1 chains pal sett3-9

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword

color bychain #1 pal sett3-9

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword

color sequential #1 chains

color sequential #1 chains palette set3-9

color sel byhetero

~select

Nothing selected

color byhetero

color sequential #1 chains palette pastel1

color byhetero

color sequential #1 chains palette accent

color byhetero

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs"

rename #3 "BFd (2fdn)"

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs"

close #1.1-7

save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs"

——— End of log from Tue Oct 8 17:54:27 2024 ———

opened ChimeraX session

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"

Chain information for PSI_BFd.opt.pdb #4
Chain	Description
?	No description available

split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828

Split PSI_BFd.opt.pdb (#4) into 6 models

Chain information for PSI_BFd.opt.pdb 1 #4.1
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 2 #4.2
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 3 #4.3
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 4 #4.4
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 5 #4.5
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 6 #4.6
Chain	Description
?	No description available

combine #4.1#4.2#4.3#4.4#4.5#4.6

Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

combine #4.1

Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'A'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

combine #4.2#4.3

Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

combine #4.2#4.4

Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

combine #4.2#4.5

Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

combine #4.2

Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

combine #4

close #4

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"

Chain information for PSI_BFd.opt.pdb #4
Chain	Description
?	No description available

split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828

Split PSI_BFd.opt.pdb (#4) into 6 models

Chain information for PSI_BFd.opt.pdb 1 #4.1
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 2 #4.2
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 3 #4.3
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 4 #4.4
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 5 #4.5
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 6 #4.6
Chain	Description
?	No description available

combine #4.2

combine #4

changechains #4.2 B

Chain IDs of 733 residues changed

changechains #4.3 C

Chain IDs of 82 residues changed

changechains #4.4 D

Chain IDs of 143 residues changed

changechains #4.5 E

Chain IDs of 67 residues changed

changechains #4.6 F

Chain IDs of 62 residues changed

renumber #4.1:1829 start 3001

1 residues renumbered

renumber #4.2 start 1

733 residues renumbered

renumber #4.3 start 1

82 residues renumbered

renumber #4.3:354-355 start 3002

2 residues renumbered

renumber #4.4 start 1

143 residues renumbered

renumber #4.5 start 1

67 residues renumbered

renumber #4.6 start 1

62 residues renumbered

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb" models #4

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb"

Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb

warnings

Start residue of secondary structure not found: HELIX 1 1 THR 36 ALA 44 1 9
Start residue of secondary structure not found: HELIX 2 2 PHE 49 HIE 52 1 4
Start residue of secondary structure not found: HELIX 3 3 LEU 56 GLY 85 1 30
Start residue of secondary structure not found: HELIX 4 4 TYR 91 ASN 96 1 6
Start residue of secondary structure not found: HELIX 5 5 GLN 114 LEU 117 1 4
180 messages similar to the above omitted

Chain information for PSI_BFd_SF4_opt.pdb
Chain	Description
5.1/?	No description available
5.2/B	No description available
5.3/C	No description available
5.4/D	No description available
5.5/E	No description available
5.6/F	No description available

combine #5.1#5.2#5.3#5.4#5.5#5.6

Remapping chain ID ' ' in PSI_BFd_SF4_opt.pdb #5.1 to 'A'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

close #5

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb"

Chain information for PSI_BFd_SF4_opt_A.pdb #5
Chain	Description
?	No description available

Chain information for PSI_BFd_SF4_opt_B.pdb #6
Chain	Description
B	No description available

combine #5#6

Remapping chain ID ' ' in PSI_BFd_SF4_opt_A.pdb #5 to 'A'
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
    residues[residues.chain_ids == chain_id].chain_ids = new_id
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
    cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop
cset(self._c_pointers, n, v)

See log for complete Python traceback.

close #6#4-5

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"

Chain information for PSI_BFd.opt.pdb #4
Chain	Description
?	No description available

split #4 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826

Split PSI_BFd.opt.pdb (#4) into 7 models

Chain information for PSI_BFd.opt.pdb 1 #4.1
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 2 #4.2
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 3 #4.3
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 4 #4.4
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 5 #4.5
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 6 #4.6
Chain	Description
?	No description available

hide #!4.7 models

hide #1 models

hide #2 models

hide #!3 models

changechains #4.2 B

Chain IDs of 733 residues changed

changechains #4.3 C

Chain IDs of 80 residues changed

changechains #4.4 D

Chain IDs of 143 residues changed

changechains #4.5 E

Chain IDs of 67 residues changed

changechains #4.6 F

Chain IDs of 60 residues changed

renumber #4.2 start 1

733 residues renumbered

renumber #4.3 start 1

80 residues renumbered

renumber #4.4 start 1

143 residues renumbered

renumber #4.5 start 1

67 residues renumbered

renumber #4.6 start 1

60 residues renumbered

changechains #4.1 A

Chain IDs of 743 residues changed

changechains #4.7 X

Chain IDs of 5 residues changed

combine #4.1#4.2#4.3#4.4#4.5#4.6

hide #!4 models

show #!4 models

combine #4.7

combine #5#6

hide #!6 models

hide #5 models

hide #!4 models

color sequential #7 chains palette accent

show #1 models

hide #1 models

color #!7 byhetero

select #7/X:1827@F2

1 atom, 1 residue, 1 model selected

close #5#4,6

rename #7 PSI_BFD_SF4_opt.pdb

rename #7 id #4

show #1 models

hide #!4 models

show #!3 models

763 atoms, 681 bonds, 8 pseudobonds, 152 residues, 3 models selected

1 atom, 1 residue, 1 model selected

select #3

762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected

show sel cartoons

select #3:cys

80 atoms, 72 bonds, 8 residues, 1 model selected

show sel atoms

color sel byhetero

hide #!3 models

show #!4 models

hide #1 models

show #!3 models

align #3:SF4 toAtoms #4:1827-1828

RMSD between 16 atom pairs is 0.346 angstroms

hide #!3 models

show #1 models

hide #1 models

select #4/X:1831 @<9 &#4/X:1827

Nothing selected

select #4/X:1831 @<10 &#4/X:1827

2 atoms, 1 pseudobond, 1 residue, 2 models selected

select #4/X:1831 @<9.2 &#4/X:1827

Nothing selected

select #4/X:1831 @<9.5 &#4/X:1827

Nothing selected

select #4/X:1831 @<9.8 &#4/X:1827

2 atoms, 1 pseudobond, 1 residue, 2 models selected

select #4/X:1831 @<9.7 &#4/X:1827

1 atom, 1 residue, 1 model selected

select #4/X:1827 @<9.7 &#4/X:1831

1 atom, 1 residue, 1 model selected

select #4/X:1831 @<9.7 &#4/X:1827

1 atom, 1 residue, 1 model selected

select #4/X:1831@F2:1827@F1

2 atoms, 2 residues, 1 model selected

select #4/X:1831@F1:1827@F2

2 atoms, 2 residues, 1 model selected

ui tool show Distances

distance #4/X:1827@F2 #4/X:1831@F1

Distance between PSI_BFD_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å

select #4/A-F

28475 atoms, 28948 bonds, 1826 residues, 1 model selected

select #4/A-F

28475 atoms, 28948 bonds, 1826 residues, 1 model selected

show sel surfaces

coulombic #4/A

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge +1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 92; net charge: 1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_A SES surface #4.2: minimum, -12.49, mean 0.00, maximum 20.13

coulombic #4/B

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 94; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_B SES surface #4.3: minimum, -15.85, mean -0.16, maximum 13.13

coulombic #4/C

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 94; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_C SES surface #4.4: minimum, -22.24, mean -4.06, maximum 8.43

coulombic #4/D

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for PSI_BFD_SF4_opt.pdb_D SES surface #4.5: minimum, -11.15, mean 2.11, maximum 15.26

coulombic #4/E

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for PSI_BFD_SF4_opt.pdb_E SES surface #4.6: minimum, -11.38, mean 1.55, maximum 11.87

coulombic #4/F

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge +0) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2); atoms read (23), bonds read (22).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 94; net charge: 0
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_F SES surface #4.7: minimum, -16.02, mean -3.74, maximum 7.04

——— End of log from Wed Oct 9 21:29:02 2024 ———

opened ChimeraX session

hide #4.7 models

hide #4.6 models

hide #4.5 models

hide #4.4 models

show #4.4 models

hide #4.4 models

hide #4.3 models

hide #4.2 models

select #4/F

829 atoms, 836 bonds, 60 residues, 1 model selected

ui tool show H-Bonds

hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true

Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt.pdb #4/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt.pdb #4/A CYF 575 SG

[Repeated 1 time(s)]

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	4 PSI_BFD_SF4_opt.pdb

21 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1  PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 HH11  2.760  1.842
PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2  PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 HH21  2.719  1.800
PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFD_SF4_opt.pdb #4/F ASP 29 O    PSI_BFD_SF4_opt.pdb #4/A LYS 31 HZ1   3.148  2.456
PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2  PSI_BFD_SF4_opt.pdb #4/A LYS 31 HZ2   2.746  1.778
PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1  PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH11  2.812  1.825
PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH11  3.358  2.560
PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2  PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH22  2.780  1.765
PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFD_SF4_opt.pdb #4/F PRO 17 O    PSI_BFD_SF4_opt.pdb #4/D LYS 109 HZ1  2.917  2.045
PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1  PSI_BFD_SF4_opt.pdb #4/D LYS 109 HZ2  2.737  1.813
PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE   PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 HE    2.875  1.950
PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1  PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH12  2.980  2.103
PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH22  2.848  1.943
PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH21  2.738  1.784
PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1  PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 HG1   2.666  1.685
PSI_BFD_SF4_opt.pdb #4/E ASN 56 ND2  PSI_BFD_SF4_opt.pdb #4/F PRO 52 O    PSI_BFD_SF4_opt.pdb #4/E ASN 56 HD22  3.598  2.755
PSI_BFD_SF4_opt.pdb #4/E ALA 67 N    PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD1  PSI_BFD_SF4_opt.pdb #4/E ALA 67 H1    3.484  2.798
PSI_BFD_SF4_opt.pdb #4/E ALA 67 N    PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 H1    2.745  1.804
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HE    2.902  1.898
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH12  2.894  1.970
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH21  3.324  2.539
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH22  2.784  1.818

21 hydrogen bonds found

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 60 items

select #4:SF4

40 atoms, 91 pseudobonds, 5 residues, 3 models selected

style sel sphere

Changed 40 atom styles

select #4/F

829 atoms, 836 bonds, 60 residues, 1 model selected

ui tool show Contacts

select #4/F &~H

430 atoms, 437 bonds, 60 residues, 1 model selected

contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

88 contacts
               atom1                                atom2                 overlap  distance
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     2.060    1.340
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.981    2.479
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    0.878    2.462
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.466    2.254
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.397    3.063
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.361    2.819
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.215    3.025
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   0.214    3.036
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    0.203    3.197
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.161    3.019
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 C     0.154    3.026
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 C     0.095    3.085
PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD   PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   0.059    3.266
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB    0.048    3.352
PSI_BFD_SF4_opt.pdb #4/F THR 7 CA    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   0.005    3.320
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ    -0.006    3.186
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.013    3.193
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.014    2.719
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 O     -0.032    3.212
PSI_BFD_SF4_opt.pdb #4/F TYR 1 O     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.032    3.272
PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1  PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.032    2.737
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.033    2.738
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.040    2.745
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2  PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.041    2.746
PSI_BFD_SF4_opt.pdb #4/F THR 7 C     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.042    3.367
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.049    3.449
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2   -0.052    3.232
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB    -0.054    3.234
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.055    2.760
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.060    3.240
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.075    2.780
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.079    2.784
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.080    3.405
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.086    2.666
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.088    3.268
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.100    3.425
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.103    3.283
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.107    2.812
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.122    3.302
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 C     -0.130    3.530
PSI_BFD_SF4_opt.pdb #4/F GLY 13 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.134    3.459
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.136    3.316
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.143    2.848
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.146    3.486
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.147    3.327
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.148    3.473
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    -0.162    3.562
PSI_BFD_SF4_opt.pdb #4/F MET 53 SD   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.167    3.649
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE    -0.170    2.875
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.177    2.902
PSI_BFD_SF4_opt.pdb #4/F GLU 8 N     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.182    3.432
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.182    3.507
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.183    3.363
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.187    3.512
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.188    3.368
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CA    -0.188    3.368
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.189    2.894
PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG   PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.197    3.522
PSI_BFD_SF4_opt.pdb #4/F PRO 17 O    PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.212    2.917
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1   -0.215    3.615
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.219    3.619
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.225    3.625
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.230    3.555
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.238    3.503
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.254    2.959
PSI_BFD_SF4_opt.pdb #4/F ALA 14 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.256    3.506
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 N     -0.272    2.977
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1   -0.275    2.980
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.275    3.735
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG    -0.291    3.691
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.299    3.499
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.301    3.626
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.316    3.716
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.323    3.723
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.332    3.657
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.337    3.662
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.342    3.542
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.346    3.671
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.353    3.753
PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.355    3.680
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.356    3.536
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.363    3.688
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 O     -0.366    3.546
PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA   PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB    -0.371    3.771
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 O     -0.372    3.332
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.376    3.776
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.389    3.789
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.394    3.719

88 contacts

contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol false select true color #ff85ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

88 contacts
               atom1                                atom2                 overlap  distance
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     2.060    1.340
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.981    2.479
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    0.878    2.462
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.466    2.254
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.397    3.063
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA    PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.361    2.819
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     0.215    3.025
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   0.214    3.036
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    0.203    3.197
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C     PSI_BFD_SF4_opt.pdb #4/E ALA 67 O     0.161    3.019
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 C     0.154    3.026
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 C     0.095    3.085
PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD   PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   0.059    3.266
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB    0.048    3.352
PSI_BFD_SF4_opt.pdb #4/F THR 7 CA    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   0.005    3.320
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ    -0.006    3.186
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.013    3.193
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.014    2.719
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 O     -0.032    3.212
PSI_BFD_SF4_opt.pdb #4/F TYR 1 O     PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.032    3.272
PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1  PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.032    2.737
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.033    2.738
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.040    2.745
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2  PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.041    2.746
PSI_BFD_SF4_opt.pdb #4/F THR 7 C     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.042    3.367
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.049    3.449
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2   -0.052    3.232
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB    -0.054    3.234
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1  PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.055    2.760
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.060    3.240
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.075    2.780
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.079    2.784
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.080    3.405
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.086    2.666
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O    PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.088    3.268
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.100    3.425
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2  PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA    -0.103    3.283
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1  PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1   -0.107    2.812
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.122    3.302
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 C     -0.130    3.530
PSI_BFD_SF4_opt.pdb #4/F GLY 13 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.134    3.459
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.136    3.316
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.143    2.848
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB    -0.146    3.486
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.147    3.327
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.148    3.473
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG    -0.162    3.562
PSI_BFD_SF4_opt.pdb #4/F MET 53 SD   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.167    3.649
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1   PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE    -0.170    2.875
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.177    2.902
PSI_BFD_SF4_opt.pdb #4/F GLU 8 N     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.182    3.432
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.182    3.507
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ    -0.183    3.363
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.187    3.512
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.188    3.368
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E SER 53 CA    -0.188    3.368
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1  PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2   -0.189    2.894
PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG   PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.197    3.522
PSI_BFD_SF4_opt.pdb #4/F PRO 17 O    PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ   -0.212    2.917
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1   -0.215    3.615
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB   PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.219    3.619
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1   -0.225    3.625
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.230    3.555
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N     PSI_BFD_SF4_opt.pdb #4/E ALA 67 N     -0.238    3.503
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O    PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.254    2.959
PSI_BFD_SF4_opt.pdb #4/F ALA 14 N    PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.256    3.506
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2   PSI_BFD_SF4_opt.pdb #4/E THR 54 N     -0.272    2.977
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O     PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1   -0.275    2.980
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB    PSI_BFD_SF4_opt.pdb #4/E ALA 67 C     -0.275    3.735
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1  PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG    -0.291    3.691
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1   -0.299    3.499
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1   -0.301    3.626
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE   PSI_BFD_SF4_opt.pdb #4/E THR 54 CB    -0.316    3.716
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E SER 53 CB    -0.323    3.723
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD    PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2   -0.332    3.657
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.337    3.662
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ   PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1   -0.342    3.542
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA   PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2   -0.346    3.671
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C    PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD    -0.353    3.753
PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA   PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2   -0.355    3.680
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2  PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ    -0.356    3.536
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG   PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ    -0.363    3.688
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C ILE 11 O     -0.366    3.546
PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA   PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB    -0.371    3.771
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O    PSI_BFD_SF4_opt.pdb #4/C LYS 34 O     -0.372    3.332
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.376    3.776
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG   PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB    -0.389    3.789
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD   PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2   -0.394    3.719

88 contacts

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone true

Assigning ribbon_hide_backbone attribute to 35 items

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 35 items

hide #4.8 models

ui tool show Clashes

select #4/F

829 atoms, 836 bonds, 60 residues, 1 model selected

clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

4 clashes
              atom1                              atom2                 overlap  distance
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N   PSI_BFD_SF4_opt.pdb #4/E ALA 67 C    2.060    1.340
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA  PSI_BFD_SF4_opt.pdb #4/E ALA 67 C    0.981    2.479
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N   PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA   0.878    2.462
PSI_BFD_SF4_opt.pdb #4/F TYR 1 H   PSI_BFD_SF4_opt.pdb #4/E ALA 67 C    0.727    2.033

4 clashes

hide #4.9 models

select #4/E

1071 atoms, 1082 bonds, 67 residues, 1 model selected

show #1 models

hide #!4 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb"

Chain information for PSI_BFd.opt.pdb #6
Chain	Description
?	No description available

split #6 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1765 atoms :1766-1826

Split PSI_BFd.opt.pdb (#6) into 7 models

Chain information for PSI_BFd.opt.pdb 1 #6.1
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 2 #6.2
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 3 #6.3
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 4 #6.4
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 5 #6.5
Chain	Description
?	No description available

Chain information for PSI_BFd.opt.pdb 6 #6.6
Chain	Description
?	No description available

changechains #6.1 A

Chain IDs of 743 residues changed

changechains #6.2 B

Chain IDs of 733 residues changed

changechains #6.3 C

Chain IDs of 80 residues changed

changechains #6.4 D

Chain IDs of 143 residues changed

changechains #6.5 E

Chain IDs of 66 residues changed

changechains #6.6 F

Chain IDs of 61 residues changed

changechains #6.7 X

Chain IDs of 5 residues changed

combine #6.1#6.2#6.3#6.4#6.5#6.6

combine #6.1#6.2#6.3#6.4#6.5#6.6#6.7

help help:user

renumber #8/A-E seqStart 1

1022 residues renumbered

hide #!6 models

hide #4.1 models

hide #1 models

hide #7 models

renumber #8/A start 1

0 residues renumbered

renumber #8/B start 1

0 residues renumbered

renumber #8/C start 1

0 residues renumbered

renumber #8/D start 1

0 residues renumbered

renumber #8/E start 1

0 residues renumbered

renumber #8/F start 1

61 residues renumbered

select #8/F

841 atoms, 848 bonds, 61 residues, 1 model selected

clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

0 clashes
atom1  atom2  overlap  distance

No clashes

clashes sel restrict #8/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

0 clashes
atom1  atom2  overlap  distance

No clashes

close #7#4-6

rename #8 id #4

close #9

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

0 clashes
atom1  atom2  overlap  distance

No clashes

color sequential #4 chains palette accent

color sel byhetero

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

select #4/F &~H

435 atoms, 442 bonds, 61 residues, 1 model selected

contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

71 contacts
           atom1                        atom2             overlap  distance
combination #4/F GLY 14 N    combination #4/C GLN 15 NE2   0.214    3.036
combination #4/F CYF 13 CB   combination #4/C GLN 15 CG    0.203    3.197
combination #4/F GLU 9 OE2   combination #4/E SER 53 C     0.154    3.026
combination #4/F GLY 50 O    combination #4/C LYS 34 C     0.095    3.085
combination #4/F GLU 19 CD   combination #4/D LYS 109 NZ   0.059    3.266
combination #4/F ILE 11 CD1  combination #4/C PRO 58 CB    0.048    3.352
combination #4/F THR 8 CA    combination #4/E ARG 43 NH2   0.005    3.320
combination #4/F ASP 30 OD1  combination #4/A ARG 27 CZ    -0.006    3.186
combination #4/F ASP 30 OD1  combination #4/A ARG 27 NH2   -0.014    2.719
combination #4/F MET 54 CE   combination #4/E THR 54 O     -0.032    3.212
combination #4/F GLU 19 OE1  combination #4/D LYS 109 NZ   -0.032    2.737
combination #4/F GLU 9 OE1   combination #4/E ARG 43 NH2   -0.033    2.738
combination #4/F ASP 30 OD2  combination #4/A LYS 31 NZ    -0.041    2.746
combination #4/F THR 8 C     combination #4/E ARG 43 NH2   -0.042    3.367
combination #4/F CYF 13 CA   combination #4/C GLN 15 CD    -0.049    3.449
combination #4/F GLU 9 OE2   combination #4/E THR 54 CG2   -0.052    3.232
combination #4/F GLY 50 O    combination #4/C LYS 34 CB    -0.054    3.234
combination #4/F ASP 30 OD1  combination #4/A ARG 27 NH1   -0.055    2.760
combination #4/F GLU 9 OE1   combination #4/E ARG 43 CZ    -0.060    3.240
combination #4/F GLU 17 OE2  combination #4/C ARG 18 NH2   -0.075    2.780
combination #4/F ARG 32 NH2  combination #4/A ASP 34 OD2   -0.079    2.784
combination #4/F GLY 14 N    combination #4/C GLN 15 CD    -0.080    3.405
combination #4/F GLU 9 OE2   combination #4/E THR 54 OG1   -0.086    2.666
combination #4/F GLU 17 CD   combination #4/C ARG 18 NH1   -0.100    3.425
combination #4/F GLU 17 OE1  combination #4/C ARG 18 NH1   -0.107    2.812
combination #4/F GLU 9 OE2   combination #4/E THR 54 CB    -0.122    3.302
combination #4/F MET 54 CE   combination #4/E THR 54 C     -0.130    3.530
combination #4/F GLY 14 C    combination #4/C GLN 15 NE2   -0.134    3.459
combination #4/F ARG 32 CZ   combination #4/A ASP 34 OD2   -0.136    3.316
combination #4/F ALA 7 O     combination #4/E ARG 43 NH2   -0.143    2.848
combination #4/F GLY 14 O    combination #4/C ARG 18 CZ    -0.147    3.327
combination #4/F CYF 13 C    combination #4/C GLN 15 NE2   -0.148    3.473
combination #4/F CYF 13 CA   combination #4/C GLN 15 CG    -0.162    3.562
combination #4/F MET 54 SD   combination #4/C ILE 11 CD1   -0.167    3.649
combination #4/F GLU 9 OE1   combination #4/E ARG 43 NE    -0.170    2.875
combination #4/F ARG 32 NE   combination #4/A THR 28 OG1   -0.177    2.902
combination #4/F GLU 9 N     combination #4/E ARG 43 NH2   -0.182    3.432
combination #4/F ASP 30 CG   combination #4/A ARG 27 NH2   -0.182    3.507
combination #4/F ALA 7 O     combination #4/E ARG 43 CZ    -0.183    3.363
combination #4/F GLU 17 CD   combination #4/C ARG 18 NH2   -0.187    3.512
combination #4/F GLU 9 OE2   combination #4/E SER 53 CB    -0.188    3.368
combination #4/F GLU 9 OE2   combination #4/E SER 53 CA    -0.188    3.368
combination #4/F ARG 32 NH1  combination #4/A ASP 34 OD2   -0.189    2.894
combination #4/F PRO 18 O    combination #4/D LYS 109 NZ   -0.212    2.917
combination #4/F PRO 53 CB   combination #4/C ILE 11 CG1   -0.215    3.615
combination #4/F CYF 13 CB   combination #4/C GLN 15 CD    -0.219    3.619
combination #4/F PRO 53 CB   combination #4/C ILE 11 CD1   -0.225    3.625
combination #4/F PRO 18 CG   combination #4/C ARG 18 NH2   -0.230    3.555
combination #4/F GLY 14 O    combination #4/C ARG 18 NH2   -0.254    2.959
combination #4/F ALA 15 N    combination #4/C GLN 15 NE2   -0.256    3.506
combination #4/F GLU 9 OE2   combination #4/E THR 54 N     -0.272    2.977
combination #4/F ALA 7 O     combination #4/E ARG 43 NH1   -0.275    2.980
combination #4/F ILE 11 CD1  combination #4/C PRO 58 CG    -0.291    3.691
combination #4/F MET 54 CE   combination #4/E THR 54 OG1   -0.299    3.499
combination #4/F ASP 30 CG   combination #4/A ARG 27 NH1   -0.301    3.626
combination #4/F MET 54 CE   combination #4/E THR 54 CB    -0.316    3.716
combination #4/F GLU 9 CD    combination #4/E SER 53 CB    -0.323    3.723
combination #4/F GLU 9 CD    combination #4/E ARG 43 NH2   -0.332    3.657
combination #4/F CYF 13 CA   combination #4/C GLN 15 NE2   -0.337    3.662
combination #4/F ARG 32 CZ   combination #4/A THR 28 OG1   -0.342    3.542
combination #4/F ASP 30 CA   combination #4/A ARG 27 NH2   -0.346    3.671
combination #4/F CYF 13 C    combination #4/C GLN 15 CD    -0.353    3.753
combination #4/F GLY 14 CA   combination #4/C GLN 15 NE2   -0.355    3.680
combination #4/F GLU 17 OE2  combination #4/C ARG 18 CZ    -0.356    3.536
combination #4/F ASP 30 CG   combination #4/A LYS 31 NZ    -0.363    3.688
combination #4/F PRO 53 CB   combination #4/C ILE 11 O     -0.366    3.546
combination #4/F VAL 51 CA   combination #4/C ALA 35 CB    -0.371    3.771
combination #4/F GLY 50 O    combination #4/C LYS 34 O     -0.372    3.332
combination #4/F PRO 53 CB   combination #4/C CYF 13 CB    -0.376    3.776
combination #4/F PRO 53 CG   combination #4/C CYF 13 CB    -0.389    3.789
combination #4/F PRO 18 CD   combination #4/C ARG 18 NH2   -0.394    3.719

71 contacts

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true

Skipping possible acceptor with bad geometry: combination #4/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor combination #4/A CYF 575 SG

[Repeated 1 time(s)]

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	4 combination

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
combination #4/A ARG 27 NH1  combination #4/F ASP 30 OD1  combination #4/A ARG 27 HH11  2.760  1.842
combination #4/A ARG 27 NH2  combination #4/F ASP 30 OD1  combination #4/A ARG 27 HH21  2.719  1.800
combination #4/A LYS 31 NZ   combination #4/F ASP 30 O    combination #4/A LYS 31 HZ1   3.148  2.456
combination #4/A LYS 31 NZ   combination #4/F ASP 30 OD2  combination #4/A LYS 31 HZ2   2.746  1.778
combination #4/C ARG 18 NH1  combination #4/F GLU 17 OE1  combination #4/C ARG 18 HH11  2.812  1.825
combination #4/C ARG 18 NH1  combination #4/F GLU 17 OE2  combination #4/C ARG 18 HH11  3.358  2.560
combination #4/C ARG 18 NH2  combination #4/F GLU 17 OE2  combination #4/C ARG 18 HH22  2.780  1.765
combination #4/D LYS 109 NZ  combination #4/F PRO 18 O    combination #4/D LYS 109 HZ1  2.917  2.045
combination #4/D LYS 109 NZ  combination #4/F GLU 19 OE1  combination #4/D LYS 109 HZ2  2.737  1.813
combination #4/E ARG 43 NE   combination #4/F GLU 9 OE1   combination #4/E ARG 43 HE    2.875  1.950
combination #4/E ARG 43 NH1  combination #4/F ALA 7 O     combination #4/E ARG 43 HH12  2.980  2.103
combination #4/E ARG 43 NH2  combination #4/F ALA 7 O     combination #4/E ARG 43 HH22  2.848  1.943
combination #4/E ARG 43 NH2  combination #4/F GLU 9 OE1   combination #4/E ARG 43 HH21  2.738  1.784
combination #4/E THR 54 OG1  combination #4/F GLU 9 OE2   combination #4/E THR 54 HG1   2.666  1.685
combination #4/E ASN 56 ND2  combination #4/F PRO 53 O    combination #4/E ASN 56 HD22  3.598  2.755
combination #4/F ARG 32 NE   combination #4/A THR 28 OG1  combination #4/F ARG 32 HE    2.902  1.898
combination #4/F ARG 32 NH1  combination #4/A ASP 34 OD2  combination #4/F ARG 32 HH12  2.894  1.970
combination #4/F ARG 32 NH2  combination #4/A THR 28 OG1  combination #4/F ARG 32 HH21  3.324  2.539
combination #4/F ARG 32 NH2  combination #4/A ASP 34 OD2  combination #4/F ARG 32 HH22  2.784  1.818

19 hydrogen bonds found

select #4

28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected

color sel byhetero

hide #4.3 models

rename #4 PSI_BFd_SF4_opt.pdb

select #4

28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 1831 items

coulombic #4/A

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge +1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 92; net charge: 1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_A SES surface #4.5: minimum, -12.49, mean 0.00, maximum 20.13

coulombic #4/B

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 94; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_B SES surface #4.6: minimum, -15.84, mean -0.16, maximum 13.13

coulombic #4/C

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2); atoms read (25), bonds read (24).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 102; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_C SES surface #4.7: minimum, -21.93, mean -4.05, maximum 8.44

coulombic #4/D

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for PSI_BFd_SF4_opt.pdb_D SES surface #4.8: minimum, -11.15, mean 2.11, maximum 15.26

coulombic #4/E

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for PSI_BFd_SF4_opt.pdb_E SES surface #4.9: minimum, -11.38, mean 1.55, maximum 11.87

coulombic #4/F

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 94; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_F SES surface #4.10: minimum, -24.55, mean -9.44, maximum 5.59

hide #4.10 models

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

ui tool show "Color Actions"

color sel dark orange target acpf

color sel byhetero target acpf

select #4/X:1831@F1:1827@F2

2 atoms, 2 residues, 1 model selected

ui tool show Distances

distance #4/X:1827@F2 #4/X:1831@F1

Distance between PSI_BFd_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å

distance style color #011993

[Repeated 2 time(s)]

distance style decimalPlaces 4

[Repeated 2 time(s)]

distance style decimalPlaces 5

[Repeated 2 time(s)]

distance style decimalPlaces 6

[Repeated 2 time(s)]

distance style decimalPlaces 5

[Repeated 2 time(s)]

distance style decimalPlaces 4

[Repeated 2 time(s)]

distance style decimalPlaces 3

[Repeated 2 time(s)]

distance style decimalPlaces 2

[Repeated 2 time(s)]

distance style decimalPlaces 1

[Repeated 2 time(s)]

distance style radius 0.3

[Repeated 2 time(s)]

distance style radius 0.2

[Repeated 2 time(s)]

hide #!5 models

select #4/F:3-9,27-34,53-61

368 atoms, 369 bonds, 24 residues, 1 model selected

show #1 models

ui tool show Matchmaker

select #2:1-2,8-24,30-47 :<0.1 &#4/F

Nothing selected

select #3:1-2,8-24,30-47 :<0.1 &#4/F

Nothing selected

select #3:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

show #!3 models

select #3:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

select #3 &~:1-2,8-24,30-47

315 atoms, 228 bonds, 114 residues, 1 model selected

color sel cyan target acpf

hide #!3 models

show #!3 models

hide #1 models

hide #!3 models

show #!3 models

hide #!3 models

show #!3 models

hide #!3 models

ui tool show Matchmaker

matchmaker #!3 to #4/F pairing bs

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3), sequence alignment score = 115.9
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)

matchmaker #!3 to #4/F pairing bs showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3), sequence alignment score = 115.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M, PSI_BFd_SF4_opt.pdb #4/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)

sequence header consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment 1

select #4:3-9,27-34,53-61

2226 atoms, 2237 bonds, 35 pseudobonds, 144 residues, 3 models selected

select #4/F:3-9,27-34,53-61

368 atoms, 369 bonds, 24 residues, 1 model selected

color sel cyan target acpf

color sel byhetero target acpf

show #4.10 models

hide #4.10 models

select #4/A:27,28,31,34

72 atoms, 69 bonds, 4 residues, 1 model selected

transparency (#!4 & sel) 20

transparency (#!4 & sel) 10

transparency (#!4 & sel) 90

select #4/C:18/D:109/E:43,54,56,67

98 atoms, 93 bonds, 5 residues, 1 model selected

transparency (#!4 & sel) 90

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

transparency (#!4 & sel) 0

select #4/A-F

28475 atoms, 28949 bonds, 90 pseudobonds, 1826 residues, 3 models selected

show #4.10 models

transparency (#!4 & sel) 30

transparency (#!4 & sel) 20

transparency (#!4 & sel) 10

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

transparency (#!4 & sel) 90

hide #4.10 models

transparency #4.1-2,4-9#!4 80

transparency #4.1-2,4-9#!4 10

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

transparency (#!4 & sel) 80

hide #4.7 models

select #4/X

40 atoms, 91 pseudobonds, 5 residues, 3 models selected

style sel sphere

Changed 40 atom styles

style sel ball

Changed 40 atom styles

show #1 models

hide #!4 models

show #!4 models

show #!5 models

hide #1 models

style sel sphere

Changed 40 atom styles

show #4.10 models

hide #4.10 models

show #4.7 models

select #4/A-E

27634 atoms, 28101 bonds, 1765 residues, 1 model selected

transparency (#!4 & sel) 30

hide #4.9 models

hide #4.8 models

hide #4.7 models

hide #4.6 models

hide #4.5 models

show #4.5 models

show #4.6 models

show #4.7 models

show #4.8 models

show #4.9 models

show #4.10 models

select add #4.10

28475 atoms, 28101 bonds, 1826 residues, 6 models selected

select subtract #4.10

27634 atoms, 28101 bonds, 1765 residues, 7 models selected

select add #4.10

28475 atoms, 28101 bonds, 1826 residues, 6 models selected

select subtract #4.10

27634 atoms, 28101 bonds, 1765 residues, 7 models selected

select add #4.10

28475 atoms, 28101 bonds, 1826 residues, 6 models selected

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

transparency (#!4 & sel) 30

hide #4.10 models

show #4.10 models

hide #4.10 models

hide #4.7 models

hide #4.9 models

hide #4.8 models

hide #4.6 models

hide #4.5 models

select #4:SF4

40 atoms, 91 pseudobonds, 5 residues, 3 models selected

style sel stick

Changed 40 atom styles

style sel ball

Changed 40 atom styles

select #4/F:42@SG

1 atom, 1 residue, 1 model selected

select #4/X:1828@F1

1 atom, 1 residue, 1 model selected

ui tool show "Build Structure"

[Repeated 1 time(s)]

help help:user

hide #4.1 models

show #4.1 models

hide #4.1 models

show #4.1 models

select #4:1828@F1

1 atom, 1 residue, 1 model selected

bond #4:1828@F1 reasonable true

Must specify two or more atoms

select #4:1828@F1,S2,S3,S4

4 atoms, 3 pseudobonds, 1 residue, 2 models selected

bond #4:1828@F1,S2,S3,S4

Created 3 bonds

bond #4:1828@F3,S1,S3,S2

Created 2 bonds

bond #4:1828@F3,S4

Created 1 bond

select #4:1828@F2,S4

2 atoms, 1 pseudobond, 1 residue, 2 models selected

select #4:1828@F2,S4,S1,S3

4 atoms, 3 pseudobonds, 1 residue, 2 models selected

bond #4:1828@F2,S4,S1,S3

Created 3 bonds

select #4:1828@F4,S2,S1,S3

4 atoms, 3 pseudobonds, 1 residue, 2 models selected

bond #4:1828@F4,S2,S1,S3

Created 3 bonds

bond #4:1828

Created 6 bonds

~bond sel

bond #4:SF4

Created 78 bonds

~bond #4:SF4@F1,F2,F3,F4

hide #4.1 models

select #4:SF4

40 atoms, 60 bonds, 91 pseudobonds, 5 residues, 3 models selected

style sel ball

Changed 40 atom styles

windowsize

window size 806 684

windowsize 750

windowsize 800

windowsize 800 600

windowsize 800 800

windowsize 800 700

windowsize 800 670

windowsize 800 675

show #4.10 models

show #4.9 models

show #4.8 models

show #4.7 models

show #4.6 models

show #4.5 models

Named views: HbondsZoom, back, front, side

view front

view side

view HbondsZoom

hide #4.10 models

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

transparency (#!4 & sel) 80

hide #4.9 models

show #4.3 models

ui tool show Contacts

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

select #4/F &~H

435 atoms, 442 bonds, 61 residues, 1 model selected

contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

71 contacts
               atom1                                atom2                 overlap  distance
PSI_BFd_SF4_opt.pdb #4/F GLY 14 N    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   0.214    3.036
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG    0.203    3.197
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E SER 53 C     0.154    3.026
PSI_BFd_SF4_opt.pdb #4/F GLY 50 O    PSI_BFd_SF4_opt.pdb #4/C LYS 34 C     0.095    3.085
PSI_BFd_SF4_opt.pdb #4/F GLU 19 CD   PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ   0.059    3.266
PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1  PSI_BFd_SF4_opt.pdb #4/C PRO 58 CB    0.048    3.352
PSI_BFd_SF4_opt.pdb #4/F THR 8 CA    PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   0.005    3.320
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 CZ    -0.006    3.186
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2   -0.014    2.719
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 O     -0.032    3.212
PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1  PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ   -0.032    2.737
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.033    2.738
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2  PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ    -0.041    2.746
PSI_BFd_SF4_opt.pdb #4/F THR 8 C     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.042    3.367
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.049    3.449
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 CG2   -0.052    3.232
PSI_BFd_SF4_opt.pdb #4/F GLY 50 O    PSI_BFd_SF4_opt.pdb #4/C LYS 34 CB    -0.054    3.234
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1   -0.055    2.760
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ    -0.060    3.240
PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.075    2.780
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2   -0.079    2.784
PSI_BFd_SF4_opt.pdb #4/F GLY 14 N    PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.080    3.405
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1   -0.086    2.666
PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1   -0.100    3.425
PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1  PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1   -0.107    2.812
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 CB    -0.122    3.302
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 C     -0.130    3.530
PSI_BFd_SF4_opt.pdb #4/F GLY 14 C    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.134    3.459
PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ   PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2   -0.136    3.316
PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.143    2.848
PSI_BFd_SF4_opt.pdb #4/F GLY 14 O    PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ    -0.147    3.327
PSI_BFd_SF4_opt.pdb #4/F CYF 13 C    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.148    3.473
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG    -0.162    3.562
PSI_BFd_SF4_opt.pdb #4/F MET 54 SD   PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1   -0.167    3.649
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE    -0.170    2.875
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE   PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1   -0.177    2.902
PSI_BFd_SF4_opt.pdb #4/F GLU 9 N     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.182    3.432
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG   PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2   -0.182    3.507
PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ    -0.183    3.363
PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.187    3.512
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E SER 53 CB    -0.188    3.368
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E SER 53 CA    -0.188    3.368
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2   -0.189    2.894
PSI_BFd_SF4_opt.pdb #4/F PRO 18 O    PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ   -0.212    2.917
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C ILE 11 CG1   -0.215    3.615
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB   PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.219    3.619
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1   -0.225    3.625
PSI_BFd_SF4_opt.pdb #4/F PRO 18 CG   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.230    3.555
PSI_BFd_SF4_opt.pdb #4/F GLY 14 O    PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.254    2.959
PSI_BFd_SF4_opt.pdb #4/F ALA 15 N    PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.256    3.506
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 N     -0.272    2.977
PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1   -0.275    2.980
PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1  PSI_BFd_SF4_opt.pdb #4/C PRO 58 CG    -0.291    3.691
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1   -0.299    3.499
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG   PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1   -0.301    3.626
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE   PSI_BFd_SF4_opt.pdb #4/E THR 54 CB    -0.316    3.716
PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD    PSI_BFd_SF4_opt.pdb #4/E SER 53 CB    -0.323    3.723
PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD    PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2   -0.332    3.657
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.337    3.662
PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ   PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1   -0.342    3.542
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CA   PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2   -0.346    3.671
PSI_BFd_SF4_opt.pdb #4/F CYF 13 C    PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD    -0.353    3.753
PSI_BFd_SF4_opt.pdb #4/F GLY 14 CA   PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2   -0.355    3.680
PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ    -0.356    3.536
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG   PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ    -0.363    3.688
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C ILE 11 O     -0.366    3.546
PSI_BFd_SF4_opt.pdb #4/F VAL 51 CA   PSI_BFd_SF4_opt.pdb #4/C ALA 35 CB    -0.371    3.771
PSI_BFd_SF4_opt.pdb #4/F GLY 50 O    PSI_BFd_SF4_opt.pdb #4/C LYS 34 O     -0.372    3.332
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB   PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB    -0.376    3.776
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CG   PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB    -0.389    3.789
PSI_BFd_SF4_opt.pdb #4/F PRO 18 CD   PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2   -0.394    3.719

71 contacts

select #4/F:14,9,50,19,11,8,30,54,19,9,17,32,7,18,53,51

199 atoms, 193 bonds, 14 residues, 1 model selected

hide sel atoms

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone true

Assigning ribbon_hide_backbone attribute to 61 items

select #4/F &H

406 atoms, 61 residues, 1 model selected

hide sel atoms

ui tool show H-Bonds

select #4/F

841 atoms, 848 bonds, 61 residues, 1 model selected

hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false select true reveal true log true

Skipping possible acceptor with bad geometry: PSI_BFd_SF4_opt.pdb #4/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor PSI_BFd_SF4_opt.pdb #4/A CYF 575 SG

[Repeated 1 time(s)]

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	4 PSI_BFd_SF4_opt.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1  PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 HH11  2.760  1.842
PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2  PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1  PSI_BFd_SF4_opt.pdb #4/A ARG 27 HH21  2.719  1.800
PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFd_SF4_opt.pdb #4/F ASP 30 O    PSI_BFd_SF4_opt.pdb #4/A LYS 31 HZ1   3.148  2.456
PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ   PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2  PSI_BFd_SF4_opt.pdb #4/A LYS 31 HZ2   2.746  1.778
PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1  PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH11  2.812  1.825
PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1  PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH11  3.358  2.560
PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2  PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2  PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH22  2.780  1.765
PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFd_SF4_opt.pdb #4/F PRO 18 O    PSI_BFd_SF4_opt.pdb #4/D LYS 109 HZ1  2.917  2.045
PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ  PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1  PSI_BFd_SF4_opt.pdb #4/D LYS 109 HZ2  2.737  1.813
PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE   PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 HE    2.875  1.950
PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1  PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH12  2.980  2.103
PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFd_SF4_opt.pdb #4/F ALA 7 O     PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH22  2.848  1.943
PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2  PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1   PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH21  2.738  1.784
PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1  PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2   PSI_BFd_SF4_opt.pdb #4/E THR 54 HG1   2.666  1.685
PSI_BFd_SF4_opt.pdb #4/E ASN 56 ND2  PSI_BFd_SF4_opt.pdb #4/F PRO 53 O    PSI_BFd_SF4_opt.pdb #4/E ASN 56 HD22  3.598  2.755
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE   PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HE    2.902  1.898
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH12  2.894  1.970
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2  PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH21  3.324  2.539
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2  PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2  PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH22  2.784  1.818

19 hydrogen bonds found

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone true

Assigning ribbon_hide_backbone attribute to 17 items

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 17 items

hide #4.3 models

show #4.9 models

show #4.10 models

hide #4.10 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png" width 1600 height 1350 supersample 3 transparentBackground true

show #4.10 models

hide #5.1 models

select add #4.10

841 atoms, 61 residues, 1 model selected

select add #4.9

1900 atoms, 127 residues, 2 models selected

select add #4.8

4177 atoms, 270 residues, 3 models selected

select add #4.7

5383 atoms, 350 residues, 4 models selected

select add #4.6

16896 atoms, 1083 residues, 5 models selected

select add #4.5

28475 atoms, 1826 residues, 6 models selected

transparency (#!4 & sel) 20

view front

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png" width 1600 height 1350 supersample 3 transparentBackground true

view side

view front

ui tool show "Color Key"

ui mousemode right "color key"

key blue-white-red :min : :-

key blue-white-red :min :0 :-

key blue-white-red :+ :0 :-

key size 0.25000,0.02000

key size 0.25000,0.01000

key fontSize 23

key fontSize 22

key fontSize 21

key fontSize 20

key fontSize 19

key fontSize 18

key ticks true

key tickThickness 5.0

key tickThickness 4.0

key labelOffset -1.0

key labelOffset -2.0

key labelOffset -3.0

key labelOffset -4.0

key labelOffset -5.0

key labelOffset -6.0

key labelOffset -7.0

key labelOffset -8.0

key labelOffset -9.0

key labelOffset -10.0

key labelOffset -11.0

key labelOffset -12.0

key labelOffset -13.0

key labelOffset -14.0

key labelOffset -15.0

key labelOffset -16.0

key labelOffset -17.0

key labelOffset -16.0

key labelOffset -15.0

key fontSize 17

key bold true

key pos 0.1,0.08000

key pos 0.70000,0.08000

key pos 0.75000,0.08000

key pos 0.75000,0.8000

key pos 0.75000,0.9000

key pos 0.75000,0.95000

windowsize 800 675

key pos 0.75000,0.90000

key pos 0.75000,0.98000

key pos 0.75000,0.9000

key pos 0.75000,0.97000

key pos 0.72000,0.97000

ui mousemode right translate

windowsize 800 675

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

view HbondsZoom

hide #4.10 models

transparency (#!4 & sel) 80

hide #6 models

show #6 models

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

transparency (#!4 & sel) 20

show #4.10 models

view front

view side

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png" width 1600 height 1350 supersample 3 transparentBackground true

——— End of log from Thu Oct 10 08:30:31 2024 ———

opened ChimeraX session

windowsize 900 675

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png" width 1800 height 1350 supersample 3 transparentBackground true

Named views: HbondsZoom, back, front, side

view front

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png" width 1800 height 1350 supersample 3 transparentBackground true

select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67

170 atoms, 162 bonds, 9 residues, 1 model selected

transparency (#!4 & sel) 80

view HbondsZoom

hide #4.10 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png" width 1800 height 1350 supersample 3 transparentBackground true

——— End of log from Fri Oct 11 10:32:45 2024 ———

opened ChimeraX session

hide #4.9 models

hide #4.7 models

hide #4.8 models

hide #4.6 models

hide #4.5 models

hide #4.4 models

show #4.4 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/@fromDROR-NAS/Prabir/PS1/PS1_dehydrogenase_docking/docking/Dock_PS1_Fd_test_output.pdb"

Chain information for Dock_PS1_Fd_test_output.pdb #7
Chain	Description
Y	No description available
Z	No description available

ui tool show Matchmaker

matchmaker #7/Z to #4/C pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFd_SF4_opt.pdb, chain C (#4) with Dock_PS1_Fd_test_output.pdb, chain Z (#7), sequence alignment score = 342.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/C, Dock_PS1_Fd_test_output.pdb #7/Z
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 80 pruned atom pairs is 0.300 angstroms; (across all 80 pairs: 0.300)

select #9:1183@S4:1741@F1

Nothing selected

select #7:1183@S4:1741@F1

2 atoms, 2 residues, 1 model selected

hide #!7 models

show #!7 models

hide #!7 models

show #!7 models

ui tool show Distances

~distance #4/X:1827@F2 #4/X:1831@F1

distance #7/Z:1741@F1 #7/Y:1183@S4

Distance between Dock_PS1_Fd_test_output.pdb #7/Z SF4 1741 F1 and /Y SF4 1183 S4: 11.458Å

select #7/Z

13593 atoms, 13984 bonds, 54 pseudobonds, 1741 residues, 2 models selected

ui tool show Clashes

clashes sel restrict #7/Y resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

9 clashes
                   atom1                                         atom2                      overlap  distance
Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH2   Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 CB    1.695    1.825
Dock_PS1_Fd_test_output.pdb #7/Z LYS 189 CG   Dock_PS1_Fd_test_output.pdb #7/Y LYS 132 NZ    1.265    2.255
Dock_PS1_Fd_test_output.pdb #7/Z ILE 11 CD1   Dock_PS1_Fd_test_output.pdb #7/Y ASP 88 OD1    0.807    2.493
Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH1   Dock_PS1_Fd_test_output.pdb #7/Y ILE 111 CG2   0.798    2.722
Dock_PS1_Fd_test_output.pdb #7/Z ILE 11 CD1   Dock_PS1_Fd_test_output.pdb #7/Y ASP 88 CG     0.795    2.965
Dock_PS1_Fd_test_output.pdb #7/Z THR 277 CG2  Dock_PS1_Fd_test_output.pdb #7/Y GLU 90 OE1    0.792    2.508
Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH2   Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 CG    0.777    2.743
Dock_PS1_Fd_test_output.pdb #7/Z THR 277 CG2  Dock_PS1_Fd_test_output.pdb #7/Y GLU 90 CD     0.702    3.058
Dock_PS1_Fd_test_output.pdb #7/Z GLU 188 O    Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 OD1   0.639    2.201

9 clashes

hide #!4 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif"

Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8
Chain	Description
A	.

ui tool show Matchmaker

matchmaker #8/A to #7/Y pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8), sequence alignment score = 139.8
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: Dock_PS1_Fd_test_output.pdb #7/Y, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 7 pruned atom pairs is 1.406 angstroms; (across all 441 pairs: 35.668)

hide #!7 models

close #8

show #!7 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif"

Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8
Chain	Description
A	.

Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 3: Dock_PS1_Fd_test_output.pdb #7/Y, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8/A

hide #8 models

save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"

——— End of log from Mon Oct 14 17:57:44 2024 ———

opened ChimeraX session

open 1hfe

1hfe title:
1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio desulfuricans [more info...]

Chain information for 1hfe #9
Chain	Description	UniProt
L M	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))	PHFL_DESVH 1-421
S T	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))	PHFS_DESVH 1-123

Non-standard residues in 1hfe #9
CMO — carbon monoxide
CYN — cyanide ion
CYS — cysteine
FE2 — Fe (II) ion
PDT — 1,3-propanedithiol
SF4 — iron/sulfur cluster
ZN — zinc ion

1hfe mmCIF Assemblies
1	author_and_software_defined_assembly
2	author_and_software_defined_assembly
3	software_defined_assembly

351 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Associated 1hfe chain L to fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25 mismatches
Associated 1hfe chain M to fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25 mismatches

show #8 models

open 6sdv

Summary of feedback from opening 6sdv fetched from pdb
note	Fetching compressed mmCIF 6sdv from http://files.rcsb.org/download/6sdv.cif

6sdv title:
W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form [more info...]

Chain information for 6sdv #10
Chain	Description	UniProt
A	Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit	Q72EJ1_DESVH 1-1005
B	Formate dehydrogenase, beta subunit, putative	Q72EJ0_DESVH 1-236

Non-standard residues in 6sdv #10
GOL — glycerol (glycerin; propane-1,2,3-triol)
H2S — hydrosulfuric acid (hydrogen sulfide)
MGD — 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)
NO3 — nitrate ion
PEG — di(hydroxyethyl)ether
SEC — selenocysteine
SF4 — iron/sulfur cluster
W — tungsten ion

hide #8 models

hide #!9 models

open "/Users/drornoy/Documents/Protein Designs/PSI H2ase/Prabir optimized structures/Dock_PS1_Fd_test_output.pdb"

Chain information for Dock_PS1_Fd_test_output.pdb #11
Chain	Description
Y	No description available
Z	No description available

Associated Dock_PS1_Fd_test_output.pdb chain Z to Dock_PS1_Fd_test_output.pdb, chain Z with 0 mismatches
Associated Dock_PS1_Fd_test_output.pdb chain Y to Dock_PS1_Fd_test_output.pdb, chain Y with 0 mismatches

show #!9 models

hide #!10 models

hide #!7 models

close #11

show #!10 models

save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"

——— End of log from Mon Oct 14 18:11:28 2024 ———

opened ChimeraX session

show #!4 models

ui tool show Matchmaker

matchmaker #9/L to #4/F pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with 1hfe, chain L (#9), sequence alignment score = 28.8
RMSD between 22 pruned atom pairs is 0.734 angstroms; (across all 52 pairs: 15.360)

select #9/M/T

4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected

hide #!4 models

hide sel cartoons

hide sel atoms

show #!4 models

hide #!4 models

show #1 models

hide #1 models

show #!4 models

hide #!4 models

show #!7 models

hide #!10 models

show #!10 models

hide #!9 models

hide #!10 models

show #!10 models

No reference and/or match structure/chain chosen

show #!4 models

hide #!10 models

hide #!7 models

show #!7 models

show #!10 models

hide #!7 models

show #!7 models

hide #!7 models

matchmaker #10/B to #7/Y pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 6sdv, chain B (#10), sequence alignment score = 1014
RMSD between 123 pruned atom pairs is 1.190 angstroms; (across all 214 pairs: 3.455)

matchmaker #9/L to #10/B pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 1.458 angstroms; (across all 188 pairs: 28.430)

show #!9 models

hide #!10 models

hide #!9 models

show #!10 models

hide #!10 models

show #!7 models

hide #!4 models

select #7/Y:1-73

585 atoms, 600 bonds, 73 residues, 1 model selected

show #!9 models

hide #!7 models

select #9/Y:25-84

Nothing selected

select #9/S:25-84

393 atoms, 400 bonds, 49 residues, 1 model selected

select #9/L:25-84

450 atoms, 461 bonds, 60 residues, 1 model selected

select #7/Y:1-73#9/L:25-84

1035 atoms, 1061 bonds, 133 residues, 2 models selected

show #!10 models

hide #!10 models

show #!7 models

matchmaker #9/L & sel to #7/Y & sel pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9), sequence alignment score = 34.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Dock_PS1_Fd_test_output.pdb #7/Y, 1hfe #9/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 8 pruned atom pairs is 1.316 angstroms; (across all 51 pairs: 12.843)

matchmaker #9/L & sel to #10/B pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment score = 34.1
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 1hfe #9/L, 6sdv #10/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 4 pruned atom pairs is 1.059 angstroms; (across all 59 pairs: 15.580)

hide #!7 models

show #!10 models

show #!7 models

hide #!10 models

hide #!9 models

show #!10 models

hide #!7 models

show #!7 models

select #7/Y:75-137#9/L:25-84

910 atoms, 928 bonds, 123 residues, 2 models selected

matchmaker #9/L & sel to #10/B & sel pairing ss showAlignment true

No 'to' chains specified

matchmaker #9/L & sel to #7/Y & sel pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9), sequence alignment score = 52.2
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: Dock_PS1_Fd_test_output.pdb #7/Y, 1hfe #9/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 22 pruned atom pairs is 1.074 angstroms; (across all 46 pairs: 6.759)

hide #!10 models

show #!9 models

hide #!9 models

show #!3 models

hide #!3 models

select #7/Y

9266 atoms, 9474 bonds, 90 pseudobonds, 1186 residues, 2 models selected

color (#!7 & sel) gray

color sel byhetero

show #!3 models

hide #!3 models

show #!9 models

hide #!7 models

show #!3 models

hide #!3 models

hide #!9 models

show #!7 models

show #!9 models

hide #!7 models

hide #!9 models

show #!7 models

align #9/L:422-423 toAtoms #7/Y:1183-1184

RMSD between 16 atom pairs is 1.724 angstroms

show #!9 models

hide #!7 models

show #!7 models

hide #!9 models

show #!9 models

hide #!9 models

hide #!7 models

show #!9 models

select #9/L:35,38,41,76, 45,66,69,72#7/Y:73,76,81,120,85,110,113,116

96 atoms, 80 bonds, 16 residues, 2 models selected

hide #!9 models

show #!7 models

select #9/L:35-41 #7/Y:73-81

114 atoms, 115 bonds, 16 residues, 2 models selected

show #!9 models

hide #!7 models

show #!3 models

hide #!9 models

show #!9 models

select ~sel & ##selected

31473 atoms, 31085 bonds, 193 pseudobonds, 5083 residues, 6 models selected

align #9/L:422-423 toAtoms #3:61,62

RMSD between 16 atom pairs is 2.679 angstroms

select #9/S:25-84

393 atoms, 400 bonds, 49 residues, 1 model selected

hide #!3 models

select #9/L:25-84

450 atoms, 461 bonds, 60 residues, 1 model selected

select #9/L:27-84

432 atoms, 442 bonds, 58 residues, 1 model selected

select #9/L:27-84

432 atoms, 442 bonds, 58 residues, 1 model selected

color sel lime

color sel byhetero

hide #!9 models

show #!7 models

select #7/Y:63-121

434 atoms, 443 bonds, 59 residues, 1 model selected

select #7/Y:72-121

354 atoms, 358 bonds, 50 residues, 1 model selected

show #!9 models

hide #!9 models

combine #3

Associated copy of BFd (2fdn) chain M to BFd (2fdn), chain M with 0 mismatches
Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M, PSI_BFd_SF4_opt.pdb #4/F, copy of BFd (2fdn) #11/M

matchmaker #11/M to #7/Y & sel pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with copy of BFd (2fdn), chain M (#11), sequence alignment score = 86.5
RMSD between 25 pruned atom pairs is 1.276 angstroms; (across all 42 pairs: 3.792)

hide #!7 models

show #!9 models

select #9/L:25-84

450 atoms, 461 bonds, 60 residues, 1 model selected

matchmaker #9/L & sel to #11/M pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker copy of BFd (2fdn), chain M (#11) with 1hfe, chain L (#9), sequence alignment score = 104.3
RMSD between 43 pruned atom pairs is 1.236 angstroms; (across all 55 pairs: 2.501)

show #!3 models

hide #!9 models

select #3:61/11:61

8 atoms, 12 bonds, 1 residue, 1 model selected

select #3:61#11:61

16 atoms, 24 bonds, 2 residues, 2 models selected

color sel cornflower blue

show #!9 models

hide #!9 models

select #9/L:25-84

450 atoms, 461 bonds, 60 residues, 1 model selected

hide #!11 models

show #!9 models

matchmaker #9/L & sel to #3/M pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker BFd (2fdn), chain M (#3) with 1hfe, chain L (#9), sequence alignment score = 104.3
RMSD between 43 pruned atom pairs is 1.232 angstroms; (across all 55 pairs: 2.484)

show #!4 models

show #8 models

matchmaker #8/A to #9/L pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker 1hfe, chain L (#9) with fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8), sequence alignment score = 2066.5
RMSD between 390 pruned atom pairs is 0.207 angstroms; (across all 396 pairs: 1.636)

hide #!9 models

show #!9 models

select #9/S

860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected

color (#!9 & sel) cyan

hide #!9 models

select #8:467-477

92 atoms, 96 bonds, 11 residues, 1 model selected

hide sel cartoons

show #!9 models

3677 atoms, 3770 bonds, 477 residues, 1 model selected

Nothing selected

hide #8 models

hide #!9 models

show #8 models

close #9-10

save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/FDH TUM/AF3 FdhF_HycB complex/fold_clj_fdhf_hycb_D8GNT2_ptm80_iptm_67/fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif"

Chain information for fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9
Chain	Description
A	.
B	.

hide #8 models

hide #!3 models

hide #!4 models

select #9:59-150 &:Cys

78 atoms, 65 bonds, 13 residues, 1 model selected

select #9:59-140 &:Cys

66 atoms, 55 bonds, 11 residues, 1 model selected

select #9/B:59-140 &:Cys

48 atoms, 40 bonds, 8 residues, 1 model selected

show #!11 models

matchmaker #9/B & sel to #11/M pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker copy of BFd (2fdn), chain M (#11) with fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif, chain B (#9), sequence alignment score = 46
RMSD between 8 pruned atom pairs is 0.685 angstroms; (across all 8 pairs: 0.685)

show #!7 models

hide #!7 models

show #!4 models

hide #!11 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"

select #9/B:112-137

195 atoms, 196 bonds, 26 residues, 1 model selected

show #!7 models

hide #!4 models

select #9/B:59-140 &:Cys

48 atoms, 40 bonds, 8 residues, 1 model selected

show sel atoms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"

——— End of log from Mon Oct 14 21:44:01 2024 ———

opened ChimeraX session

hide #!5 models

hide #5.1 models

hide #6 models

hide #!7 models

hide #9 models

show #!4 models

open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.pdb

Chain information for DdHyd_PSI.opt.pdb #10
Chain	Description
?	No description available

ui tool show Matchmaker

matchmaker #!10 to #4 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFd_SF4_opt.pdb, chain A (#4) with DdHyd_PSI.opt.pdb, chain (blank) (#10), sequence alignment score = 3958.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/A, DdHyd_PSI.opt.pdb #10/?
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 743 pruned atom pairs is 0.000 angstroms; (across all 743 pairs: 0.000)

hide #!4 models

split #10 atoms :1-743,2239 atoms :744-1476 atoms :1477-1556,2240-2241 atoms :1557-1699 atoms :1700-1765 atoms :1766-2238,2242-2244

Split DdHyd_PSI.opt.pdb (#10) into 6 models

Chain information for DdHyd_PSI.opt.pdb 1 #10.1
Chain	Description
?	No description available

Chain information for DdHyd_PSI.opt.pdb 2 #10.2
Chain	Description
?	No description available

Chain information for DdHyd_PSI.opt.pdb 3 #10.3
Chain	Description
?	No description available

Chain information for DdHyd_PSI.opt.pdb 4 #10.4
Chain	Description
?	No description available

Chain information for DdHyd_PSI.opt.pdb 5 #10.5
Chain	Description
?	No description available

Chain information for DdHyd_PSI.opt.pdb 6 #10.6
Chain	Description
?	No description available

Associated DdHyd_PSI.opt.pdb 1 (10.1) chain (blank) to PSI_BFd_SF4_opt.pdb, chain A with 0 mismatches
Associated DdHyd_PSI.opt.pdb 2 (10.2) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 3 (10.3) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 4 (10.4) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 5 (10.5) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 6 (10.6) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149, in invoke
    return self._func(self._name, data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 427, in <lambda>
    self.associate([s for s in models if isinstance(s, AtomicStructure)], force=False))
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 394, in associate
    self._notify_observers(note_name, note_data)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 826, in _notify_observers
    self._notify_rmsd_change()
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 835, in _notify_rmsd_change
    self._notify_observers(self.NOTE_RMSD_UPDATE, None)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 823, in _notify_observers
    recipient.alignment_notification(note_name, note_data)
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_headers/rmsd.py", line 52, in alignment_notification
    self.reevaluate()
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_headers/rmsd.py", line 126, in reevaluate
    new_eval_chains = self.alignment.rmsd_chains
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 670, in rmsd_chains
    rmsd = self._eval_rmsd([c1, c2])
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 769, in _eval_rmsd
    for coords in self._gather_coords(chains, pa_name):
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 794, in _gather_coords
    pa = r.find_atom(pa_name)
         ^^^^^^^^^^^^^^^^^^^^
  File "atomic_cpp/cymol.pyx", line 1651, in chimerax.atomic.cymol.CyResidue.find_atom
RuntimeError: Residue already deleted

Error processing trigger "add models":
RuntimeError: Residue already deleted

File "atomic_cpp/cymol.pyx", line 1651, in chimerax.atomic.cymol.CyResidue.find_atom

See log for complete Python traceback.

hide #!10.1 models

hide #10.2 models

hide #!10.3 models

hide #10.4 models

hide #10.5 models

hide #!10.6 models

show #!10.1 models

hide #!10.1 models

show #10.2 models

show #!10.1 models

hide #10.2 models

hide #!10.1 models

show #!10.1 models

show #10.2 models

show #!10.3 models

show #10.4 models

hide #!10.3 models

hide #10.2 models

hide #!10.1 models

hide #10.4 models

show #10.5 models

hide #10.5 models

show #!10.6 models

show #10.2 models

show #!10.1 models

show #!10.3 models

show #10.4 models

show #10.5 models

ui tool show "Change Chain IDs"

select add #10.1

11635 atoms, 11818 bonds, 18 pseudobonds, 752 residues, 3 models selected

changechains sel A

Cannot reassign chain ID to only part of polymeric chain (fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9/B)

select add #10.1

11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected

changechains sel A

Chain IDs of 744 residues changed

select subtract #10.1

Nothing selected

select add #10.2

11513 atoms, 11725 bonds, 733 residues, 1 model selected

changechains sel B

Chain IDs of 733 residues changed

select subtract #10.2

Nothing selected

select add #10.3

1222 atoms, 1219 bonds, 36 pseudobonds, 82 residues, 2 models selected

changechains sel C

Chain IDs of 82 residues changed

select subtract #10.3

Nothing selected

select add #10.4

2277 atoms, 2308 bonds, 143 residues, 1 model selected

changechains sel D

Chain IDs of 143 residues changed

select subtract #10.4

Nothing selected

select add #10.5

1059 atoms, 1071 bonds, 66 residues, 1 model selected

changechains sel E

Chain IDs of 66 residues changed

select add #10.6

8232 atoms, 8313 bonds, 54 pseudobonds, 542 residues, 3 models selected

select subtract #10.5

7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected

changechains sel F

Chain IDs of 476 residues changed

34831 atoms, 35343 bonds, 108 pseudobonds, 2244 residues, 10 models selected

color sel bychain

color sel byhetero

[Repeated 1 time(s)]

combine #10.1#10.2#10.3#10.4#10.5#10.6

Associated combination chain A to PSI_BFd_SF4_opt.pdb, chain A with 0 mismatches
Associated combination chain B to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated combination chain F to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated combination chain D to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated combination chain C to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches
Associated combination chain E to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches

hide #!10 models

show #!10 models

rename #12 "DdHyd_PSI.opt.pdb split to chains"

close #10

rename #12 id #10

select #10/A-E

27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected

ui tool show Clashes

clashes sel restrict #10/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true

Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False

0 clashes
atom1  atom2  overlap  distance

No clashes

ui tool show Contacts

select #10/A-E &~H

14013 atoms, 14456 bonds, 54 pseudobonds, 1768 residues, 2 models selected

contacts sel restrict "#10/F &~H" resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true

Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False

61 contacts
                       atom1                                                 atom2                          overlap  distance
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 C     0.260    3.065
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CA    0.258    2.922
DdHyd_PSI.opt.pdb split to chains #10/E ALA 1728 CB   DdHyd_PSI.opt.pdb split to chains #10/F THR 1767 CG2   0.154    3.246
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 N     0.146    3.104
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 OE1  DdHyd_PSI.opt.pdb split to chains #10/F PRO 1816 CB    0.120    3.060
DdHyd_PSI.opt.pdb split to chains #10/C ILE 1487 O    DdHyd_PSI.opt.pdb split to chains #10/F PRO 1841 CB    0.119    3.061
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 C     0.116    3.209
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 CG    0.093    3.232
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C     0.079    3.246
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CA    0.072    3.253
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N     0.044    3.281
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N     0.010    3.315
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 O     -0.010    3.190
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 C     -0.035    3.215
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CB    -0.041    3.366
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O     -0.057    2.762
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O     -0.077    3.257
DdHyd_PSI.opt.pdb split to chains #10/C ARG 1494 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 NE2   -0.098    3.348
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2   -0.100    2.805
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 CZ   DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2   -0.106    3.286
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 C     -0.107    3.507
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C     -0.117    3.517
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1   -0.124    2.829
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2   -0.130    2.835
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1   -0.134    2.839
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1795 N     -0.145    3.395
DdHyd_PSI.opt.pdb split to chains #10/D VAL 1666 CG1  DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 O     -0.150    3.330
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CA    -0.155    3.555
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N     -0.157    2.862
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CA    -0.160    3.485
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O     -0.161    2.866
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1512 CE   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2157 OH    -0.167    3.367
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O     -0.168    2.873
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 O     -0.177    2.882
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N     -0.197    2.902
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N     -0.199    3.449
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 CB    -0.209    3.534
DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N    DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O     -0.210    2.915
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 OE1  DdHyd_PSI.opt.pdb split to chains #10/F PRO 1816 CG    -0.212    3.392
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CD    -0.217    3.542
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CB   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 ND2   -0.237    3.562
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 C     -0.249    3.574
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 CA    -0.265    3.665
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1512 CD   DdHyd_PSI.opt.pdb split to chains #10/F TYR 2157 OH    -0.269    3.469
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1   -0.279    2.984
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NE   DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 CA    -0.285    3.610
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N     -0.292    3.542
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CG   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1   -0.295    3.475
DdHyd_PSI.opt.pdb split to chains #10/D VAL 1666 O    DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 O     -0.301    3.261
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CA    -0.304    3.704
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C     -0.317    3.642
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ   DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O     -0.322    3.502
DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 C     -0.340    3.740
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 CD   DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CA    -0.345    3.745
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F THR 1767 OG1   -0.349    3.074
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 N     -0.360    3.685
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CG    -0.363    3.688
DdHyd_PSI.opt.pdb split to chains #10/E GLN 1731 CB   DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 NZ    -0.363    3.688
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F GLY 1795 CA    -0.364    3.689
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CG   DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CG2   -0.368    3.768
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 C     -0.398    3.723

61 contacts

hide #10.3 models

ui tool show H-Bonds

hbonds sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true

Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to chains #10/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split to chains #10/A CYF 575 SG

[Repeated 1 time(s)]

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	10 DdHyd_PSI.opt.pdb split to chains

13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 NH2    DdHyd_PSI.opt.pdb split to chains #10/F GLU 1814 OE1  DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 HH21    3.498  2.750
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O    DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 HE21  2.873  2.126
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1  DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 HZ2   2.829  1.880
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1  DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ2   2.839  1.911
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O    DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ1   2.762  1.871
DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N    DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O    DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 H3    2.915  1.906
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH11  2.866  1.886
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH21  3.207  2.381
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH12  2.805  1.855
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.984  2.083
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.835  1.934
DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.862  2.132
DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.902  1.907

13 hydrogen bonds found

select #10/A-E

27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected

hbonds sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	10 DdHyd_PSI.opt.pdb split to chains

13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 NH2    DdHyd_PSI.opt.pdb split to chains #10/F GLU 1814 OE1  DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 HH21    3.498  2.750
DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2  DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O    DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 HE21  2.873  2.126
DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ   DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1  DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 HZ2   2.829  1.880
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1  DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ2   2.839  1.911
DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ   DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O    DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ1   2.762  1.871
DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N    DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O    DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 H3    2.915  1.906
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH11  2.866  1.886
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2  DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O    DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH21  3.207  2.381
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH12  2.805  1.855
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.984  2.083
DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2  DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2  DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22  2.835  1.934
DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.862  2.132
DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N    DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2  DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1    2.902  1.907

13 hydrogen bonds found

select #10/A-F

34831 atoms, 35343 bonds, 182 pseudobonds, 2244 residues, 4 models selected

hide sel cartoons

hide #10.1 models

help help:user

bonds #10:2239-2244@F4@F2

Unknown command: bonds #10:2239-2244@F4@F2

bond #10:2239-2244@F4@F2

Created 6 bonds

select #10:2239-2244

48 atoms, 6 bonds, 108 pseudobonds, 6 residues, 2 models selected

style sel stick

Changed 48 atom styles

~bond #10:2239-2244@F4@F2

~bond #10:2239-2244@F4@S1

bond #10:2239-2244@F4@S1

Created 6 bonds

bond #10:2239-2244@F3@S1

Created 6 bonds

bond #10:2239-2244@F3@S2

Created 6 bonds

bond #10:2239-2244@F4@S2

Created 6 bonds

bond #10:2239-2244@F3@S4

Created 6 bonds

bond #10:2239-2244@F2@S4

Created 6 bonds

bond #10:2239-2244@F2@S1

Created 6 bonds

bond #10:2239-2244@F2@S3

Created 6 bonds

bond #10:2239-2244@F4@S3

Created 6 bonds

bond #10:2239-2244@F1@S2

Created 6 bonds

bond #10:2239-2244@F1@S3

Created 6 bonds

bond #10:2239-2244@F1@S4

Created 6 bonds

select #10:SF4

48 atoms, 72 bonds, 108 pseudobonds, 6 residues, 2 models selected

style sel ball

Changed 48 atom styles

select #10:SF4 &Fe

24 atoms, 36 pseudobonds, 6 residues, 2 models selected

style sel sphere

Changed 24 atom styles

select #10

34831 atoms, 35415 bonds, 183 pseudobonds, 2244 residues, 5 models selected

show sel cartoons

show #!4 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs"

——— End of log from Mon Oct 21 23:18:11 2024 ———

opened ChimeraX session

hide #!4 models

show #!4 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb" models #4

close session

open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.chains.pdb "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb"

Chain information for DdHyd_PSI.opt.chains.pdb #1
Chain	Description
A	No description available
B	No description available
C	No description available
D	No description available
E	No description available
F	No description available

Chain information for PSI_BFD_SF4_opt_chains.pdb #2
Chain	Description
A	No description available
B	No description available
C	No description available
D	No description available
E	No description available
F	No description available

select protein

63258 atoms, 64292 bonds, 4064 residues, 2 models selected

hide sel atoms

show sel cartoons

color sel bychain

color sel byhetero

~select

Nothing selected

color byhetero

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs"

——— End of log from Tue Oct 22 09:43:01 2024 ———

opened ChimeraX session

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

hide #!1 models

show #!1 models

rename #1 id #3

rename #2 id #1

rename #3 id #2

open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb

Chain information for ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb #3
Chain	Description
A	No description available
B	No description available
C	No description available
D	No description available
E	No description available
F	No description available
G	No description available

select #3 &protein

34578 atoms, 35179 bonds, 2662 residues, 1 model selected

hide sel atoms

show sel cartoons

select #3/Y:1183-1187,1200

41 atoms, 12 bonds, 72 pseudobonds, 6 residues, 2 models selected

hide #!2 models

hide #!1 models

style sel sphere

Changed 41 atom styles

color sel byhetero

select #3/Z:SF4

24 atoms, 54 pseudobonds, 3 residues, 2 models selected

color sel byhetero

select #3

34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected

color sel bychain

color sel byhetero

select #13/Y:1188-1189

Nothing selected

select #3/Y:1188-1189

94 atoms, 104 bonds, 2 residues, 1 model selected

color sel magenta

color sel byhetero

show #!2 models

show #!1 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs"

——— End of log from Tue Oct 22 11:39:31 2024 ———

opened ChimeraX session

34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected

Nothing selected

hide #!3 models

hide #!2 models

show #!3 models

show #!2 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs"

——— End of log from Tue Oct 22 11:40:52 2024 ———

view name session-start

opened ChimeraX session

hide #!2 models

hide #!3 models

open 2fdn

2fdn title:
2[4FE-4S] ferredoxin from clostridium acidi-urici [more info...]

Chain information for 2fdn #4
Chain	Description	UniProt
A	FERREDOXIN	FER_CLOAC 1-55

Non-standard residues in 2fdn #4
SF4 — iron/sulfur cluster

74 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.

ui tool show Matchmaker

matchmaker #!4 to #1

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4), sequence alignment score = 115.9
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)

select #1/A-E

27634 atoms, 28101 bonds, 1765 residues, 1 model selected

hide sel cartoons

select #1/X

40 atoms, 90 pseudobonds, 5 residues, 2 models selected

hide sel atoms

undo

select #1/X:1829-1831

24 atoms, 54 pseudobonds, 3 residues, 2 models selected

hide sel atoms

select #1/X:1827-1828

16 atoms, 36 pseudobonds, 2 residues, 2 models selected

style sel stick

Changed 16 atom styles

hide #!4 models

select #1/F:Cys

Nothing selected

select #1/F:Cyf

80 atoms, 72 bonds, 8 residues, 1 model selected

show sel atoms

style sel stick

Changed 80 atom styles

45159 atoms, 5877 residues, 4 models selected

hide sel & #!1 atoms

show #!4 models

select #1/X:1827-1828

16 atoms, 36 pseudobonds, 2 residues, 2 models selected

style sel sphere

Changed 16 atom styles

hide #!1 models

select #4:61-62

16 atoms, 24 bonds, 2 residues, 1 model selected

style sel sphere

Changed 16 atom styles

hide #4.1 models

show #!1 models

ui tool show Matchmaker

matchmaker #!4 to #1 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4), sequence alignment score = 115.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: PSI_BFD_SF4_opt_chains.pdb #1/F, 2fdn #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)

select #1/F:3

14 atoms, 14 bonds, 1 residue, 1 model selected

select #1/F:3-8

96 atoms, 96 bonds, 6 residues, 1 model selected

select #1/F:3

14 atoms, 14 bonds, 1 residue, 1 model selected

select #1/F:3-8 #4/A:3-8

168 atoms, 167 bonds, 12 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [3-8] RMSD: 6.436

color sel cyan

select #1/F:9

15 atoms, 14 bonds, 1 residue, 1 model selected

select #1/F:9

15 atoms, 14 bonds, 1 residue, 1 model selected

color sel cyan

select #4/A:25

6 atoms, 5 bonds, 1 residue, 1 model selected

select #1/F:27-34 #4/A:25-29

160 atoms, 159 bonds, 13 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [27-34] RMSD: 4.473

color sel cyan

select #4/A:48

14 atoms, 14 bonds, 1 residue, 1 model selected

select #1/F:53-61 #4/A:48-55

240 atoms, 242 bonds, 17 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [53-62] RMSD: 5.761

color sel cyan

hide #!4 models

show #!4 models

hide #!1 models

color sel & #!4 byhetero

color #!4 byhetero

select #1/F:3

14 atoms, 14 bonds, 1 residue, 1 model selected

select #1/F:3-9 #4/A:3-8

183 atoms, 182 bonds, 13 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [3-9] RMSD: 6.436

show sel & #!4 atoms

style sel & #!4 stick

Changed 72 atom styles

select #4/A:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

select #4/A:1-55 &~:1-2,8-24,30-47

205 atoms, 204 bonds, 18 residues, 1 model selected

show sel atoms

45159 atoms, 5877 residues, 4 models selected

hide sel & #!4 atoms

select #4/A:1-55 &~:1-2,8-24,30-47

205 atoms, 204 bonds, 18 residues, 1 model selected

select #1/F:3

14 atoms, 14 bonds, 1 residue, 1 model selected

select #1/F:3-9

111 atoms, 111 bonds, 7 residues, 1 model selected

select #4/A:1-55 &~:1-2,8-24,30-47#1/F:3-9

205 atoms, 204 bonds, 18 residues, 1 model selected

select #4/A:1-55 &~:1-2,8-24,30-47 |#1/F:3-9

205 atoms, 209 bonds, 18 residues, 1 model selected

select #1/F:3-9,27-34,53-61

368 atoms, 369 bonds, 24 residues, 1 model selected

show #!1 models

show sel atoms

style sel stick

Changed 368 atom styles

color sel byhetero

45159 atoms, 5877 residues, 4 models selected

hide sel & #!1,4 atoms

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 5877 items

select @N,O

13656 atoms, 6875 residues, 4 models selected

hide sel & #!1,4 atoms

hide #!4 models

show #!4 models

hide #!1 models

show #!1 models

hide #!4 models

show #!4 models

hide #!4 models

show #!4 models

hide #!1 models

show #!1 models

hide #!4 models

select #4/A:1-2,8-24,30-47

447 atoms, 448 bonds, 37 residues, 1 model selected

show #!4 models

hide #!1 models

ui tool show "Color Actions"

color sel light slate gray

color sel steel blue

color sel olive drab

color sel steel blue

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

hide #!4 models

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs"

——— End of log from Sat Sep 13 22:23:04 2025 ———

view name session-start

opened ChimeraX session

select #1/A-E

27634 atoms, 28101 bonds, 1765 residues, 1 model selected

show sel cartoons

select #1/X:1827-1828

16 atoms, 36 pseudobonds, 2 residues, 2 models selected

select #1/X

40 atoms, 90 pseudobonds, 5 residues, 2 models selected

show sel atoms

select #1/F

841 atoms, 848 bonds, 61 residues, 1 model selected

ui tool show H-Bonds

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true

Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG

[Repeated 1 time(s)]

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	1 PSI_BFD_SF4_opt_chains.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818

19 hydrogen bonds found

show sel atoms

style sel stick

Changed 31 atom styles

ui tool show H-Bonds

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	1 PSI_BFD_SF4_opt_chains.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818

19 hydrogen bonds found

select #1/F

841 atoms, 848 bonds, 61 residues, 1 model selected

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	1 PSI_BFD_SF4_opt_chains.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818

19 hydrogen bonds found

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	1 PSI_BFD_SF4_opt_chains.pdb

19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11  2.760  1.842
PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1  PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21  2.719  1.800
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O    PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1   3.148  2.456
PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ   PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2  PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2   2.746  1.778
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  2.812  1.825
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11  3.358  2.560
PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2  PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22  2.780  1.765
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O    PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1  2.917  2.045
PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1  PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2  2.737  1.813
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE   PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE    2.875  1.950
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12  2.980  2.103
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O     PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22  2.848  1.943
PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1   PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21  2.738  1.784
PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2   PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1   2.666  1.685
PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2  PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O    PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22  3.598  2.755
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE   PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE    2.902  1.898
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12  2.894  1.970
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21  3.324  2.539
PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2  PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2  PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22  2.784  1.818

19 hydrogen bonds found

select #1/A:27,28,31,34/C:18/D:109/E:43,54,56

170 atoms, 162 bonds, 9 residues, 1 model selected

select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &~H

81 atoms, 73 bonds, 9 residues, 1 model selected

show sel atoms

style sel stick

Changed 81 atom styles

hide #1.2.1 models

select #1/X:1829-1831

24 atoms, 54 pseudobonds, 3 residues, 2 models selected

style sel ball

Changed 24 atom styles

style sel sphere

Changed 24 atom styles

select #1/X:1829-1831 &S

12 atoms, 3 residues, 1 model selected

ui tool show "Color Actions"

color sel gold

color sel goldenrod

color sel gold

color sel green yellow

color sel yellow green

color sel green yellow

color sel pale goldenrod

color sel wheat

[Repeated 1 time(s)]

color sel beige

color sel light goldenrod yellow

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Graphics/Designs/BFD design on PSI H-bonds.png" width 1800 height 1355 supersample 3 transparentBackground true

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"

view name zoom1

ui tool show "Color Actions"

select #1/A &protein

11579 atoms, 11778 bonds, 743 residues, 1 model selected

color sel thistle target c

color sel lavender target c

color sel light pink target c

color sel thistle target c

color sel plum target c

select #1/B &protein

11513 atoms, 11725 bonds, 733 residues, 1 model selected

color sel light pink target c

select #1/C &protein

1206 atoms, 1219 bonds, 80 residues, 1 model selected

color sel pale green target c

color sel dark sea green target c

select #1/C &protein

1206 atoms, 1219 bonds, 80 residues, 1 model selected

color sel dark gray target c

color sel gray target c

color sel teal target c

color sel green target c

color sel maroon target c

color sel dark salmon target c

color sel dark goldenrod target c

color sel brown target c

select #1/D &protein

2277 atoms, 2308 bonds, 143 residues, 1 model selected

color sel dark khaki target c

color sel wheat target c

color sel peach puff target c

color sel pale goldenrod target c

color sel light salmon target c

color sel burly wood target c

select #1/E &protein

1059 atoms, 1071 bonds, 66 residues, 1 model selected

view zoom1

view name zoom2

select #1/E &protein

1059 atoms, 1071 bonds, 66 residues, 1 model selected

color sel sandy brown target c

color sel peach puff target c

color sel light salmon target c

[Repeated 1 time(s)]

color sel sandy brown target c

color sel light salmon target c

view name zoom2

select #1/F:17-18

29 atoms, 29 bonds, 2 residues, 1 model selected

select #1/F:17-18 &~H

16 atoms, 16 bonds, 2 residues, 1 model selected

show sel atoms

style sel stick

Changed 16 atom styles

select #1/F:17-19 &~H

25 atoms, 25 bonds, 3 residues, 1 model selected

show sel atoms

style sel stick

Changed 25 atom styles

select #1/C

1206 atoms, 1219 bonds, 80 residues, 1 model selected

select #1/C &protein

1206 atoms, 1219 bonds, 80 residues, 1 model selected

color sel brown target ac

color sel byhetero

color sel orange red target c

color sel dark orange target c

color sel coral target c

color sel chocolate target c

select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &~H

81 atoms, 73 bonds, 9 residues, 1 model selected

color sel steel blue target c

color sel steel blue target ac

color sel byhetero

color sel medium orchid target ac

color sel byhetero

color sel medium purple target ac

color sel byhetero

name frozen Hbonding sel

color sel medium violet red target ac

color sel deep pink target ac

color sel byhetero

select #1/E &protein

1059 atoms, 1071 bonds, 66 residues, 1 model selected

color sel bisque target c

color sel pink target c

color sel peach puff target c

select #1/C &protein

1206 atoms, 1219 bonds, 80 residues, 1 model selected

color sel wheat target c

color sel burly wood target c

color sel tan target c

[Repeated 1 time(s)]

select #1/D &protein

2277 atoms, 2308 bonds, 143 residues, 1 model selected

color sel burly wood target c

select #1/F:9,17-19 &~H

34 atoms, 33 bonds, 4 residues, 1 model selected

show sel atoms

view name zoom2

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"

——— End of log from Sun Sep 14 07:49:27 2025 ———

view name session-start

opened ChimeraX session

show #!2 models

hide #!1 models

show #!1 models

hide #!2 models

show #!2 models

hide #!2 models

ui tool show "Selection Inspector"

select #1/A:393

16 atoms, 15 bonds, 1 residue, 1 model selected

show #!2 models

select #2/A

11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected

help help:user

color #2/A DDA0DD target c

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword

color #2/A #DDA0DD target c

select #1/B:393

20 atoms, 20 bonds, 1 residue, 1 model selected

color #2/B #FFB6C1 target c

select #1/C:40

11 atoms, 10 bonds, 1 residue, 1 model selected

color #2/C #D2B48C target c

view session_start

Expected an objects specifier or a view name or a keyword

Named views: session-start, zoom1, zoom2

view session-start

select #1/D:40

14 atoms, 14 bonds, 1 residue, 1 model selected

hide #!1 models

show #!1 models

hide #!1 models

show #!1 models

select #2/D:40

Nothing selected

hide #!1 models

Named views: session-start, zoom1, zoom2

view session-start

select #1/D:40

14 atoms, 14 bonds, 1 residue, 1 model selected

color #2/D #DEB887 target c

select #1/E:40

16 atoms, 15 bonds, 1 residue, 1 model selected

show #!1 models

hide #!1 models

color #2/D #FFDAB9 target c

color #2/D #DEB887 target c

color #2/E #FFDAB9 target c

show #!1 models

hide #!1 models

show #!1 models

hide #!1 models

select #1/X:1829@S1

1 atom, 1 residue, 1 model selected

select #2:2239-2241

24 atoms, 54 pseudobonds, 3 residues, 2 models selected

select #2:2239-2241 &S

12 atoms, 3 residues, 1 model selected

select #1/X:1829@S1

1 atom, 1 residue, 1 model selected

select #2:2239-2241 &S

12 atoms, 3 residues, 1 model selected

color #2:2239-2241 &S #FAFAD2

view session-start

view name viewH2ase

open 1hfe

1hfe title:
1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio desulfuricans [more info...]

Chain information for 1hfe #5
Chain	Description	UniProt
L M	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))	PHFL_DESVH 1-421
S T	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))	PHFS_DESVH 1-123

Non-standard residues in 1hfe #5
CMO — carbon monoxide
CYN — cyanide ion
CYS — cysteine
FE2 — Fe (II) ion
PDT — 1,3-propanedithiol
SF4 — iron/sulfur cluster
ZN — zinc ion

1hfe mmCIF Assemblies
1	author_and_software_defined_assembly
2	author_and_software_defined_assembly
3	software_defined_assembly

351 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.

ui tool show Matchmaker

matchmaker #!5 to #2

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)

select #5/M/T

4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected

select #5/L/S

4358 atoms, 3871 bonds, 19 pseudobonds, 1080 residues, 2 models selected

select #5/M/T

4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected

hide sel cartoons

hide sel atoms

select #5/S

860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected

color (#!5 & sel) orange

color sel byhetero

select #2/F:2157

21 atoms, 21 bonds, 1 residue, 1 model selected

select #2/F:2157-2238

1309 atoms, 1329 bonds, 82 residues, 1 model selected

ui tool show "Color Actions"

color sel steel blue

color sel slate gray

color sel light slate gray

color sel steel blue

color sel light steel blue

select #2/F:2150-2151

14 atoms, 13 bonds, 2 residues, 1 model selected

select #5:386

8 atoms, 6 bonds, 2 residues, 1 model selected

select #5:388

18 atoms, 16 bonds, 2 residues, 1 model selected

select #2/F:2152-2153

22 atoms, 21 bonds, 2 residues, 1 model selected

select #2/F:2152-2156

65 atoms, 65 bonds, 5 residues, 1 model selected

color sel cyan

select #2/F:388-390

Nothing selected

select #5/L:388-390

23 atoms, 23 bonds, 3 residues, 1 model selected

color sel orange

color sel orange red

select #5/L:388-397

71 atoms, 72 bonds, 10 residues, 1 model selected

color sel orange

color sel byhetero

select #5/M:43-123

607 atoms, 624 bonds, 81 residues, 1 model selected

color sel light steel blue

select #5/S:43-123

651 atoms, 670 bonds, 81 residues, 1 model selected

color sel light steel blue

select #5/:15-30,35-52,58-387,396-477

Expected an objects specifier or a keyword

select #5/L:15-30,35-52,58-387,396-477

2866 atoms, 2890 bonds, 18 pseudobonds, 423 residues, 2 models selected

hide #!2 models

show #!1 models

hide #!1 models

show #!2 models

select #5/L:1-400 &~15-30,35-52,58-387,396-477

Expected a keyword

select #5/L:1-400 &~:15-30,35-52,58-387,396-477

240 atoms, 241 bonds, 30 residues, 1 model selected

color sel cyan

color sel byhetero

hide #!5 models

view viewH2ase

show #!5 models

select #2/F:1766-1776

160 atoms, 160 bonds, 11 residues, 1 model selected

select #2/F:1766-1775

146 atoms, 146 bonds, 10 residues, 1 model selected

hide #!2 models

show #!2 models

select #2/F:1766-1775,1792-1795,1814-1821

293 atoms, 293 bonds, 22 residues, 1 model selected

color sel cyan

color sel byhetero

view viewH2ase

hide #!5 models

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"

select #2/F &protein

7149 atoms, 7242 bonds, 473 residues, 1 model selected

ui tool show H-Bonds

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true

Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG

[Repeated 1 time(s)]

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2 DdHyd_PSI.opt.chains.pdb

13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_PSI.opt.chains.pdb #2/A ARG 27 NH2    DdHyd_PSI.opt.chains.pdb #2/F GLU 1814 OE1  DdHyd_PSI.opt.chains.pdb #2/A ARG 27 HH21    3.498  2.750
DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 NE2  DdHyd_PSI.opt.chains.pdb #2/F CYF 1799 O    DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 HE21  2.873  2.126
DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 NZ   DdHyd_PSI.opt.chains.pdb #2/F ASN 1843 OD1  DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 HZ2   2.829  1.880
DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F GLN 1804 OE1  DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ2   2.839  1.911
DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F PRO 2234 O    DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ1   2.762  1.871
DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 N    DdHyd_PSI.opt.chains.pdb #2/F LYS 2032 O    DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 H3    2.915  1.906
DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH1  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH11  2.866  1.886
DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH2  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH21  3.207  2.381
DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH1  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH12  2.805  1.855
DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD1  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.984  2.083
DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.835  1.934
DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD1  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.862  2.132
DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD2  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.902  1.907

13 hydrogen bonds found

select #2/F &protein

7149 atoms, 7242 bonds, 473 residues, 1 model selected

select #2 &protein

34783 atoms, 35343 bonds, 13 pseudobonds, 2238 residues, 2 models selected

style sel stick

Changed 34783 atom styles

select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730

161 atoms, 154 bonds, 8 residues, 1 model selected

ui tool show "Color Actions"

color sel deep pink

color sel byhetero

select #2 &H

17179 atoms, 2238 residues, 1 model selected

hide sel atoms

ui tool show H-Bonds

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2 DdHyd_PSI.opt.chains.pdb

0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):

0 hydrogen bonds found

select #2/F &protein

7149 atoms, 7242 bonds, 473 residues, 1 model selected

ui tool show H-Bonds

hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true

Skipped 2 atom(s) with bad connectivities; see log for details

Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
	2 DdHyd_PSI.opt.chains.pdb

13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_PSI.opt.chains.pdb #2/A ARG 27 NH2    DdHyd_PSI.opt.chains.pdb #2/F GLU 1814 OE1  DdHyd_PSI.opt.chains.pdb #2/A ARG 27 HH21    3.498  2.750
DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 NE2  DdHyd_PSI.opt.chains.pdb #2/F CYF 1799 O    DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 HE21  2.873  2.126
DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 NZ   DdHyd_PSI.opt.chains.pdb #2/F ASN 1843 OD1  DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 HZ2   2.829  1.880
DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F GLN 1804 OE1  DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ2   2.839  1.911
DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ   DdHyd_PSI.opt.chains.pdb #2/F PRO 2234 O    DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ1   2.762  1.871
DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 N    DdHyd_PSI.opt.chains.pdb #2/F LYS 2032 O    DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 H3    2.915  1.906
DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH1  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH11  2.866  1.886
DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH2  DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O    DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH21  3.207  2.381
DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH1  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH12  2.805  1.855
DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD1  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.984  2.083
DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2  DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2  DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22  2.835  1.934
DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD1  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.862  2.132
DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N    DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD2  DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1    2.902  1.907

13 hydrogen bonds found

show sel atoms

hide #2.2.1 models

color #2/E #FFDAB9 target c

color #2/D #DEB887 target c

color #2/C #D2B48C target c

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"

Named views: session-start, viewH2ase, zoom1, zoom2

view session-start

color #2/A #DDA0DD target c

view name viewH2aseHbonds

[Repeated 1 time(s)]

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"

——— End of log from Mon Sep 15 19:12:58 2025 ———

view name session-start

opened ChimeraX session

view viewH2aseHbonds

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd Hbonds.png" width 1800 height 1358 supersample 3 transparentBackground true

select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730

161 atoms, 154 bonds, 8 residues, 1 model selected

name frozen HbondingDdH sel

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"

——— End of log from Mon Sep 15 20:51:36 2025 ———

view name session-start

opened ChimeraX session

select #2/F:1766-1775,1792-1795,1814-1821 &H

139 atoms, 22 residues, 1 model selected

select #2/F:1766-1775,1792-1795,1814-1821 &~H

154 atoms, 154 bonds, 22 residues, 1 model selected

show sel atoms

select #2/F:1766-1775,1792-1795,1814-1821,2151-2156 &~H

196 atoms, 196 bonds, 28 residues, 1 model selected

select #2/F:1766-1775,1792-1795,1814-1821,2152-2156 &~H

192 atoms, 192 bonds, 27 residues, 1 model selected

show sel atoms

color sel byhetero

view session-start

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"

——— End of log from Mon Sep 15 21:24:55 2025 ———

view name session-start

opened ChimeraX session

select #2/C-F &protein

11691 atoms, 11840 bonds, 12 pseudobonds, 762 residues, 2 models selected

coulombic sel

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2); atoms read (25), bonds read (24).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 102; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.10.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for DdHyd_PSI.opt.chains.pdb_C SES surface #2.3: minimum, -22.19, mean -4.05, maximum 8.43
Coulombic values for DdHyd_PSI.opt.chains.pdb_D SES surface #2.4: minimum, -10.22, mean 2.11, maximum 15.27
Coulombic values for DdHyd_PSI.opt.chains.pdb_E SES surface #2.5: minimum, -11.34, mean 1.57, maximum 12.31
Coulombic values for DdHyd_PSI.opt.chains.pdb_F SES surface #2.6: minimum, -23.25, mean -3.85, maximum 11.53
To also show corresponding color key, enter the above coulombic command and add key true

view name coulSide

select #2/A-B &protein

23092 atoms, 23503 bonds, 1476 residues, 1 model selected

coulombic sel

Using Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYF)
(CYF) Welcome to antechamber 20.0: molecular input file processor.
(CYF)
(CYF)

Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2); atoms read (22), bonds read (21).

(CYF) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(CYF)
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(CYF) Info: Total number of electrons: 94; net charge: -1
(CYF)
(CYF) Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(CYF)
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.10.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1

(CYF)
(CYF)

Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(CYF)
Charges for residue CYF determined
Coulombic values for DdHyd_PSI.opt.chains.pdb_A SES surface #2.7: minimum, -12.58, mean -0.47, maximum 17.74
Coulombic values for DdHyd_PSI.opt.chains.pdb_B SES surface #2.8: minimum, -15.68, mean -0.16, maximum 13.13
To also show corresponding color key, enter the above coulombic command and add key true

hide #2.6 models

combine #5

hide #!2 models

select #6/L:CMO,CYN,PDT,FE2:424

23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected

hide sel atoms

show sel atoms

select #6 &~/L:CMO,CYN,PDT,FE2:424

8705 atoms, 7722 bonds, 29 pseudobonds, 2164 residues, 2 models selected

hide sel cartoons

hide sel atoms

delete atoms (#!6 & sel)

delete bonds (#!6 & sel)

show #!2 models

align #6/L:424@FE4,S3,FE1,S2,S1,FE2,S4,FE3 toAtoms #2/F:2244@F4,S3,F1,S2,S1,F2,S4,F3

RMSD between 8 atom pairs is 0.065 angstroms

select #2/F:CYF

120 atoms, 108 bonds, 12 residues, 1 model selected

show sel atoms

select #2/F:CYF &H

48 atoms, 12 residues, 1 model selected

hide sel atoms

select #2/F:SF4

24 atoms, 54 pseudobonds, 3 residues, 2 models selected

style sel ball

Changed 24 atom styles

select #6:SF4

8 atoms, 12 bonds, 1 residue, 1 model selected

hide sel atoms

select #2/F:SF4

24 atoms, 54 pseudobonds, 3 residues, 2 models selected

style sel sphere

Changed 24 atom styles

select #6

23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected

ui tool show "Color Actions"

color sel maroon

color sel byhetero

style sel sphere

Changed 23 atom styles

show #2.6 models

hide #2.3 models

hide #2.4 models

hide #2.5 models

show #2.3 models

show #2.4 models

show #2.5 models

save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design coulombic surfs.cxs"

close #1

close #4

rename #6 "Catalytic Site"

ui tool show Matchmaker

close #3

matchmaker #5/L to #2/F pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F, 1hfe #5/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)

matchmaker #5/L to #2/F pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains.pdb #2/F, 1hfe #5/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)

hide #2.3 models

show #2.3 models

hide #2.6 models

hide #2.7 models

hide #2.8 models

show #2.8 models

show #2.7 models

show #!5 models

select #2/F:1812

20 atoms, 20 bonds, 1 residue, 1 model selected

select #2/F:1812-1820 #5/L:51-56

164 atoms, 166 bonds, 15 residues, 2 models selected
MatchMaker Alignment [ID: 2] region chain F..chain L [51-59] RMSD: 2.042

select #2/F:1766

21 atoms, 20 bonds, 1 residue, 1 model selected

select #2/F:1766-1773 #5/L:3-12

213 atoms, 212 bonds, 18 residues, 2 models selected
MatchMaker Alignment [ID: 2] region chain F..chain L [3-12] RMSD: 8.370

hide #!5 models

show #2.6 models

hide #2.6 models

select #5/L:389

7 atoms, 7 bonds, 1 residue, 1 model selected

select #5/L:389-391

22 atoms, 22 bonds, 3 residues, 1 model selected

select #2/F:2149

7 atoms, 6 bonds, 1 residue, 1 model selected

select #2/F:2149-2152

28 atoms, 27 bonds, 4 residues, 1 model selected

select #2/F:2152

7 atoms, 6 bonds, 1 residue, 1 model selected

select #2/F:2152-2153

22 atoms, 21 bonds, 2 residues, 1 model selected

select #2/F:2152

7 atoms, 6 bonds, 1 residue, 1 model selected

select #2/F:2152-2155

50 atoms, 50 bonds, 4 residues, 1 model selected

select #2/F:2152

7 atoms, 6 bonds, 1 residue, 1 model selected

select #2/F:2152-2156

65 atoms, 65 bonds, 5 residues, 1 model selected

show #!5 models

ui tool show Matchmaker

matchmaker #5/L to #2/F pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

save "/Users/drornoy/OneDrive - Migal/ISF-DFG/PSI-DdHyd design.cxs"

——— End of log from Wed Sep 17 15:57:48 2025 ———

view name session-start

opened ChimeraX session

hide #!5 models

hide #!6 models

show #!5 models

hide #!5 models

show #!6 models

hide #!6 models

show #!5 models

hide #!5 models

show #!5 models

select #5/L:2-3

17 atoms, 16 bonds, 2 residues, 1 model selected

hide #!5 models

show #!5 models

hide #!5 models

show #!5 models

hide #!5 models

select #5/L:389

7 atoms, 7 bonds, 1 residue, 1 model selected

select #5/L:389-391

22 atoms, 22 bonds, 3 residues, 1 model selected

show #!5 models

select #2/F:2153

15 atoms, 14 bonds, 1 residue, 1 model selected

select #2/F:2153-2158

96 atoms, 97 bonds, 6 residues, 1 model selected

select #5/L:388-389

16 atoms, 16 bonds, 2 residues, 1 model selected

select #5/L:389-398

63 atoms, 64 bonds, 10 residues, 1 model selected

open 3lx4

Summary of feedback from opening 3lx4 fetched from pdb
note	Fetching compressed mmCIF 3lx4 from http://files.rcsb.org/download/3lx4.cif

3lx4 title:
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG) [more info...]

Chain information for 3lx4 #1
Chain	Description	UniProt
A B	Fe-hydrogenase	Q9FYU1_CHLRE 17-457

Non-standard residues in 3lx4 #1
ACT — acetate ion
CL — chloride ion
SF4 — iron/sulfur cluster

3lx4 mmCIF Assemblies
1	author_and_software_defined_assembly
2	author_and_software_defined_assembly

32 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.

ui tool show Matchmaker

matchmaker #!1 to #2

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 3lx4, chain B (#1), sequence alignment score = 861.9
RMSD between 264 pruned atom pairs is 1.082 angstroms; (across all 356 pairs: 3.848)

hide #2.8 models

hide #2.7 models

show #2.6 models

hide #2.6 models

show #2.7 models

hide #2.7 models

hide #2.3 models

hide #2.4 models

hide #2.5 models

show #2.6 models

hide #2.6 models

show #2.5 models

show #2.4 models

show #2.3 models

hide #2.3 models

show #2.7 models

show #2.8 models

hide #!2 models

hide #!5 models

show #!2 models

hide #!2 models

select #1/A

3460 atoms, 3157 bonds, 7 pseudobonds, 774 residues, 3 models selected

hide sel cartoons

hide sel atoms

show #!2 models

ui tool show "Show Sequence Viewer"

sequence chain #5/S #5/T

Alignment identifier is 2

[Repeated 1 time(s)]

show #!5 models

hide #!2 models

hide #!1 models

[Repeated 1 time(s)]

select #5/S-T:38

18 atoms, 16 bonds, 2 residues, 1 model selected

select #5/S-T:38-45

140 atoms, 140 bonds, 16 residues, 1 model selected

select #5/S-T:46

22 atoms, 20 bonds, 2 residues, 1 model selected

select #5/S-T:46-51

100 atoms, 100 bonds, 12 residues, 1 model selected

select #5/S-T:38

18 atoms, 16 bonds, 2 residues, 1 model selected

select #5/S-T:38-45

140 atoms, 140 bonds, 16 residues, 1 model selected

select #5/L:2-14

115 atoms, 116 bonds, 13 residues, 1 model selected

select #5/L:2-14,31-34,53-57

183 atoms, 183 bonds, 22 residues, 1 model selected

select #5/L:2-14,31-34,53-57,388-397

254 atoms, 255 bonds, 32 residues, 1 model selected

ui tool show "Color Actions"

color sel alice blue

color sel sky blue

color sel light sky blue

color sel light blue

color sel pale turquoise

color sel light steel blue

color sel pale turquoise

color sel wheat

color sel gainsboro

color sel powder blue

color sel pale turquoise

color sel byhetero

show #!2 models

hide #!2 models

show #!2 models

select #5/L:2-14,31-34,53-57,388-397/S:36-42

316 atoms, 317 bonds, 39 residues, 1 model selected

select #5/L:2-14,31-34,53-57,388-397/S:36-41

304 atoms, 304 bonds, 38 residues, 1 model selected

hide #!5 models

save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs"

close #1

rename #1 id 1

rename #2 id 1

rename #1 id 2

help help:user

rename #2#6 id #1

rename #1 DdHyd_PSI

rename #5 id #2

show #!1.2 models

combine #1 copy t

Expected a keyword

combine #1

Associated combination chain F to chain F with 0 mismatches
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #1.1/F, 1hfe #2/L, combination #3/F

hide #3.1 models

show #3.1 models

hide #!1 models

hide #!3 models

show #!3 models

hide #3.1 models

hide #3.2 models

help help:user

[Repeated 1 time(s)]

split #3 chains

Split combination (#3) into 7 models

Chain information for combination A #3.1
Chain	Description
A	No description available

Chain information for combination B #3.2
Chain	Description
B	No description available

Chain information for combination C #3.3
Chain	Description
C	No description available

Chain information for combination D #3.4
Chain	Description
D	No description available

Chain information for combination E #3.5
Chain	Description
E	No description available

Chain information for combination F #3.6
Chain	Description
F	No description available

Associated combination F (3.6) chain F to chain F with 0 mismatches
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #1.1/F, 1hfe #2/L, combination F #3.6/F

hide #!3.1 models

hide #3.2 models

hide #!3.3 models

hide #3.4 models

hide #3.5 models

show #!1 models

select #3.1-3.3

Nothing selected

select #3.1

11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected

select #3.1#3.2

23100 atoms, 23503 bonds, 18 pseudobonds, 1477 residues, 3 models selected

rename #3.1#3.2#3.3#3.4#3.5 id #4

show #1.1.3 models

hide #1.1.3 models

select #1/F

7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected

select #1.1/F

7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected

hide sel atoms

hide sel cartoons

hide #!1 models

hide #!3 models

show #!3 models

show #!1 models

hide #!1 models

show #!1 models

select #1.1/F

7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected

delete atoms (#!1.1 & sel)

Chains used in RMSD evaluation for alignment 1: 1hfe #2/L, combination F #3.6/F

delete bonds (#!1.1 & sel)

hide #!1.1 models

show #!1.1 models

hide #!1.1 models

show #!1.1 models

close #1.2

rename #1.1 id #1

rename #1.1 id 1

combine #1.1

hide #!4 models

hide #!1 models

close #5

show #!1 models

hide #!1.1 models

show #!1.1 models

rename #1 PSI

rename #1.1 "DdHyd_PSI.opt.chains no DdHyd"

rename #2 id 6

show #!4 models

hide #!1 models

hide #!4 models

show #!4 models

show #!4.1 models

show #4.2 models

show #!4.3 models

show #4.4 models

show #4.5 models

close #4

show #!1 models

rename #3.6 DdHyd_PSI.opt.chains

rename #3.7 "Catalytic site"

rename #3 id 2

rename #6 id 3

rename #2 DdHyd_PSI

hide #!1 models

show #!3 models

open 9gbu 9gnk

Summary of feedback from opening 9gbu fetched from pdb
warnings	Atom HS2 is not in the residue template for 402 /A:505 Atom HS2 is not in the residue template for 402 /B:504
notes	Fetching compressed mmCIF 9gbu from http://files.rcsb.org/download/9gbu.cif Fetching CCD MPD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif

Summary of feedback from opening 9gnk fetched from pdb
warnings	Atom HS2 is not in the residue template for 402 /A:502 Atom H3 is not in the residue template for PG4 /A:512
notes	Fetching compressed mmCIF 9gnk from http://files.rcsb.org/download/9gnk.cif Fetching CCD EPE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif Fetching CCD PG4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif

9gbu title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei [more info...]

Chain information for 9gbu #4
Chain	Description	UniProt
A B	Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	PHFL_NITV2 1-389, PHFS_NITV2 403-480

Non-standard residues in 9gbu #4
402 — dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
MPD — (4S)-2-methyl-2,4-pentanediol
SF4 — iron/sulfur cluster

9gbu mmCIF Assemblies
1	author_defined_assembly
2	author_defined_assembly

166 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
9gnk title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum [more info...]

Chain information for 9gnk #5
Chain	Description	UniProt
A	Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	PHFL_NITV2 1-390, PHFS_NITV2 404-482

Non-standard residues in 9gnk #5
402 — dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
CMO — carbon monoxide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SF4 — iron/sulfur cluster

9gnk mmCIF Assemblies
1	author_defined_assembly

200 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Associated 9gbu chain A to chain L with 31 mismatches
Associated 9gbu chain B to chain L with 31 mismatches
Associated 9gnk chain A to chain L with 29 mismatches
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F, 1hfe #3/L, 9gbu #4/B, 9gnk #5/A

hide #!4 models

show #!4 models

hide #!5 models

select #4/B

7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected

hide sel cartoons

hide sel atoms

show #!5 models

matchmaker #!4-5 to #2.6

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gbu, chain A (#4), sequence alignment score = 2182.6
RMSD between 454 pruned atom pairs is 0.553 angstroms; (across all 469 pairs: 1.405)

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gnk, chain A (#5), sequence alignment score = 2184.3
RMSD between 453 pruned atom pairs is 0.534 angstroms; (across all 470 pairs: 1.482)

Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F, 1hfe #3/L, 9gbu #4/A, 9gnk #5/A

hide #!3 models

show #!3 models

hide #!3 models

show #!3 models

16271 atoms, 15290 bonds, 63 pseudobonds, 2749 residues, 4 models selected

select add #4

23871 atoms, 22854 bonds, 87 pseudobonds, 3365 residues, 4 models selected

select subtract #4

8728 atoms, 7742 bonds, 39 pseudobonds, 2172 residues, 2 models selected

Nothing selected

select add #5

8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected

hide #!4 models

hide #!3 models

hide #!2 models

color sel sandy brown

color sel byhetero

show #!4 models

show #!3 models

show #!2 models

color sel dark khaki

color sel plum

color sel byhetero

select subtract #5

Nothing selected

hide #!4 models

hide #!3 models

hide #!2 models

select :4O2

Nothing selected

select :402

64 atoms, 61 bonds, 4 residues, 3 models selected

select #5:402

22 atoms, 21 bonds, 1 residue, 1 model selected

select ::name="402"

72 atoms, 48 bonds, 33 pseudobonds, 3 residues, 4 models selected

select :EPE,PEG,PG4,MPD

290 atoms, 278 bonds, 13 residues, 2 models selected

hide sel & #!5 atoms

select :EPE,PEG,PG4,MPD,HOH

2233 atoms, 278 bonds, 1956 residues, 3 models selected

hide sel & #!5 atoms

show #!4 models

show #!2 models

hide #!2 models

ui tool show "Show Sequence Viewer"

sequence chain #5/A

Alignment identifier is 5/A

sequence chain #4/A #4/B

Alignment identifier is 3

select #5/A:400

12 atoms, 11 bonds, 1 residue, 1 model selected

select #5/A:388

17 atoms, 16 bonds, 1 residue, 1 model selected

select #5/A:388-400

209 atoms, 210 bonds, 13 residues, 1 model selected

select #5/A:390

16 atoms, 15 bonds, 1 residue, 1 model selected

select #5/A:390-399

166 atoms, 166 bonds, 10 residues, 1 model selected

select #4/A-B:402

22 atoms, 20 bonds, 2 residues, 1 model selected

select #4/A-B:390-402

440 atoms, 442 bonds, 26 residues, 1 model selected

select #5/A:404-405

36 atoms, 35 bonds, 2 residues, 1 model selected

select #5/A:390-405

277 atoms, 277 bonds, 16 residues, 1 model selected

select #5/A:390-391

32 atoms, 31 bonds, 2 residues, 1 model selected

select #5/A:390-404

253 atoms, 253 bonds, 15 residues, 1 model selected

select #5/A:390-404#4/A:390-402

473 atoms, 474 bonds, 28 residues, 2 models selected

show #!2 models

select #4/A:390-402

220 atoms, 221 bonds, 13 residues, 1 model selected

color sel sea green

select #5/A:390-404

253 atoms, 253 bonds, 15 residues, 1 model selected

color sel purple

show #!3 models

save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs"

——— End of log from Wed Oct 22 18:27:07 2025 ———

view name session-start

opened ChimeraX session

open "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_model_0.cif"

Chain information for fold_ddhyab_model_0.cif #6
Chain	Description
A	.

Associated fold_ddhyab_model_0.cif chain A to chain L with 27 mismatches
Computing secondary structure

hide #!5 models

hide #!4 models

hide #!2 models

ui tool show Matchmaker

matchmaker #6 to #2.6

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with fold_ddhyab_model_0.cif, chain A (#6), sequence alignment score = 2224.5
RMSD between 456 pruned atom pairs is 0.436 angstroms; (across all 470 pairs: 1.221)

ui tool show "AlphaFold Error Plot"

alphafold pae #6 file "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_full_data_0.json"

color bfactor #6 palette alphafold

3649 atoms, 474 residues, atom bfactor range 50.4 to 99

hide #!3 models

show #!5 models

show #!4 models

show #!2 models

show #!1 models

hide #!1 models

save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs"

——— End of log from Wed Oct 22 19:01:49 2025 ———

view name session-start

opened ChimeraX session

hide #!5 models

hide #!4 models

hide #!2 models

show #!2 models

show #!1 models

hide #!2 models

show #!2 models

hide #!2 models

hide #!1 models

show #!3 models

hide #6 models

show #!1 models

show #!2 models

close #6

select add #5

8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected

select subtract #5

Nothing selected

help help:user

rename #5 id 9

rename #4 id 8

rename #3 id 7

save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif"

Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3
Chain	Description
A	.

Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to chain L with 25 mismatches
Computing secondary structure

hide #!1 models

hide #!7 models

ui tool show Matchmaker

matchmaker #3 to #2.6 showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3), sequence alignment score = 2230.1
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: DdHyd_PSI.opt.chains #2.6/F, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 456 pruned atom pairs is 0.422 angstroms; (across all 470 pairs: 1.377)

ui tool show "AlphaFold Error Plot"

alphafold pae #3 file "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_full_data_0.json"

color bfactor #3 palette alphafold

3677 atoms, 477 residues, atom bfactor range 44.8 to 99

3677 atoms, 3770 bonds, 477 residues, 1 model selected

color sel byhetero

Nothing selected

show #!7 models

show #!8 models

hide #!7 models

hide #!8 models

open 3lx4

3lx4 title:
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG) [more info...]

Chain information for 3lx4 #4
Chain	Description	UniProt
A B	Fe-hydrogenase	Q9FYU1_CHLRE 17-457

Non-standard residues in 3lx4 #4
ACT — acetate ion
CL — chloride ion
SF4 — iron/sulfur cluster

3lx4 mmCIF Assemblies
1	author_and_software_defined_assembly
2	author_and_software_defined_assembly

32 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.

select :SF4

192 atoms, 216 bonds, 108 pseudobonds, 24 residues, 9 models selected

ui tool show Matchmaker

matchmaker #4/A to #2.6/F pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 3lx4, chain A (#4), sequence alignment score = 854.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains #2.6/F, 3lx4 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 265 pruned atom pairs is 1.087 angstroms; (across all 356 pairs: 3.844)

rename #4 "CrHydA1 3lx4"

rename #7 "DdHydAHydB 1hfe"

select #3/B

Nothing selected

select #4/B

3507 atoms, 3157 bonds, 7 pseudobonds, 821 residues, 3 models selected

hide sel cartoons

hide sel atoms

close #8

close #9

show #!7 models

hide #!7 models

rename #7 id 5

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

open 8ru6

Summary of feedback from opening 8ru6 fetched from pdb
warning	Atom HS1 is not in the residue template for MHX /B:508

8ru6 title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum [more info...]

Chain information for 8ru6 #6
Chain	Description	UniProt
B	Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit	PHFL_DESVH 1-392, PHF1_CLOPA 393-396, PHFS_DESVH 397-481

Non-standard residues in 8ru6 #6
MHX — Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form)
PG4 — tetraethylene glycol
SF4 — iron/sulfur cluster

147 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Associated 8ru6 chain B to chain L with 25 mismatches

hide #!4 models

hide #3 models

hide #!2 models

show #!2 models

show #3 models

show #!4 models

ui tool show Matchmaker

matchmaker #6/B to #3/A pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with 8ru6, chain B (#6), sequence alignment score = 2480.9
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 8ru6 #6/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 471 pruned atom pairs is 0.353 angstroms; (across all 475 pairs: 0.476)

hide #!2 models

hide #3 models

show #!5 models

show #3 models

hide #3 models

show #3 models

hide #!4 models

hide #!5 models

rename #6 "DdHydAB_L1 8ru6"

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

open 9gnk

Summary of feedback from opening 9gnk fetched from pdb
warnings	Atom HS2 is not in the residue template for 402 /A:502 Atom H3 is not in the residue template for PG4 /A:512

9gnk title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum [more info...]

Chain information for 9gnk #7
Chain	Description	UniProt
A	Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	PHFL_NITV2 1-390, PHFS_NITV2 404-482

Non-standard residues in 9gnk #7
402 — dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
CMO — carbon monoxide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SF4 — iron/sulfur cluster

9gnk mmCIF Assemblies
1	author_defined_assembly

200 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Associated 9gnk chain A to chain L with 29 mismatches

ui tool show Matchmaker

matchmaker #7/A to #3/A pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with 9gnk, chain A (#7), sequence alignment score = 2461.4
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 9gnk #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 469 pruned atom pairs is 0.373 angstroms; (across all 476 pairs: 0.928)

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

open 9gbu

Summary of feedback from opening 9gbu fetched from pdb
warnings	Atom HS2 is not in the residue template for 402 /A:505 Atom HS2 is not in the residue template for 402 /B:504

Chain information for 9gbu #8
Chain	Description	UniProt
A B	Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	PHFL_NITV2 1-389, PHFS_NITV2 403-480

Non-standard residues in 9gbu #8
402 — dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
MPD — (4S)-2-methyl-2,4-pentanediol
SF4 — iron/sulfur cluster

9gbu mmCIF Assemblies
1	author_defined_assembly
2	author_defined_assembly

166 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Associated 9gbu chain A to chain L with 31 mismatches
Associated 9gbu chain B to chain L with 31 mismatches

matchmaker #6/B to #3/A pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with DdHydAB_L1 8ru6, chain B (#6), sequence alignment score = 2480.9
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, DdHydAB_L1 8ru6 #6/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 471 pruned atom pairs is 0.353 angstroms; (across all 475 pairs: 0.476)

matchmaker #8/A to #3/A pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with 9gbu, chain A (#8), sequence alignment score = 2453.1
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 9gbu #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 469 pruned atom pairs is 0.356 angstroms; (across all 475 pairs: 0.810)

select #8/B

7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected

hide sel cartoons

hide sel atoms

hide #!7 models

hide #!6 models

hide #!8 models

show #!8 models

show #!7 models

rename #7 "DdHydAB_L2 9gnk"

rename #8 "DdHydAB_L3 9gbu"

select :PG4

179 atoms, 172 bonds, 7 residues, 2 models selected

hide sel & #!7 atoms

select :MPD

132 atoms, 126 bonds, 6 residues, 1 model selected

hide sel atoms

select :HOH

3198 atoms, 3198 residues, 5 models selected

hide sel & #!7-8 atoms

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

show #!6 models

ui tool show "Color Actions"

select #8

15143 atoms, 15112 bonds, 48 pseudobonds, 1193 residues, 2 models selected

show #!4 models

color sel plum

color sel byhetero

color sel magenta

color sel byhetero

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

select :PG4

179 atoms, 172 bonds, 7 residues, 2 models selected

hide sel atoms

select :PG4,HOH

3377 atoms, 172 bonds, 3205 residues, 5 models selected

hide sel & #!4,6-8 atoms

ui tool show Matchmaker

matchmaker #4/A to #3/A pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with CrHydA1 3lx4, chain A (#4), sequence alignment score = 943.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, CrHydA1 3lx4 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 268 pruned atom pairs is 1.062 angstroms; (across all 361 pairs: 3.707)

matchmaker #4/A to #3/A pairing ss showAlignment true

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with CrHydA1 3lx4, chain A (#4), sequence alignment score = 943.4
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, CrHydA1 3lx4 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
RMSD between 268 pruned atom pairs is 1.062 angstroms; (across all 361 pairs: 3.707)

select #3/A:392

7 atoms, 6 bonds, 1 residue, 1 model selected

select #3/A:392-393 #4/A:391-392

30 atoms, 28 bonds, 4 residues, 2 models selected
MatchMaker Alignment [ID: 7] region chain A..chain A [451-452] RMSD: 1.147

help help:user

view name All_H2ases

select #3/A:392

7 atoms, 6 bonds, 1 residue, 1 model selected

select #3/A:392-393 #4/A:391-392

30 atoms, 28 bonds, 4 residues, 2 models selected
MatchMaker Alignment [ID: 2] region chain A..chain A [451-452] RMSD: 1.147

view All_H2ases

show #!2 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

hide #!6 models

hide #!7 models

hide #!8 models

hide #!4 models

select #2.6/F:2153-2156 #3/A:389-395

112 atoms, 112 bonds, 11 residues, 2 models selected
MatchMaker Alignment [ID: 4] region chain F..chain A [392-398] RMSD: 7.546

show #!1 models

show #1.1.3 models

hide #1.1.3 models

show #!6 models

show #!7 models

show #!8 models

view name PsaC_interface

save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs"

——— End of log from Wed Oct 29 10:26:11 2025 ———

view name session-start

opened ChimeraX session

hide #!1 models

hide #!2 models

show #!2 models

hide #!1.1 models

show #!1.1 models

hide #!2 models

hide #!6 models

hide #!7 models

hide #!8 models

hide #!1 models

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif"

Chain information for HydAB_TD_linker_model.cif #9
Chain	Description
A	.

No chain in structure corresponds to chain ID given in local score info (chain 'B')

Associated HydAB_TD_linker_model.cif chain A to chain L with 25 mismatches
Associated HydAB_TD_linker_model.cif chain A to chain A with 0 mismatches
[Repeated 4 time(s)]Computing secondary structure

rename #9 HydAB_TD_linker_model_MSA.cif

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif"

Chain information for HydAB_TD_linker_model.cif #10
Chain	Description
A	.

No chain in structure corresponds to chain ID given in local score info (chain 'B')

Associated HydAB_TD_linker_model.cif chain A to chain L with 25 mismatches
Associated HydAB_TD_linker_model.cif chain A to chain A with 0 mismatches
[Repeated 4 time(s)]Computing secondary structure

rename #10 HydAB_TD_linker_model_noMSA.cif

ui tool show AlphaFold

ui tool show "AlphaFold Error Plot"

alphafold pae #9 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json"

color bfactor #9 palette alphafold

3720 atoms, 481 residues, atom bfactor range 41.5 to 99

ui tool show "AlphaFold Error Plot"

alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json"

color bfactor #10 palette alphafold

3720 atoms, 481 residues, atom bfactor range 13.2 to 97

ui tool show "AlphaFold Error Plot"

alphafold pae #9 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json"

color bfactor #9 palette alphafold

3720 atoms, 481 residues, atom bfactor range 41.5 to 99

color bfactor #9 palette alphafold

3720 atoms, 481 residues, atom bfactor range 41.5 to 99

ui tool show Matchmaker

matchmaker #!9-10 to #2.6

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with HydAB_TD_linker_model_MSA.cif, chain A (#9), sequence alignment score = 2218.3
RMSD between 458 pruned atom pairs is 0.496 angstroms; (across all 470 pairs: 1.251)

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with HydAB_TD_linker_model_noMSA.cif, chain A (#10), sequence alignment score = 1834.3
RMSD between 35 pruned atom pairs is 1.452 angstroms; (across all 470 pairs: 19.133)

hide #!9 models

show #!9 models

hide #!9 models

show #!9 models

3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected

7552 atoms, 7744 bonds, 22 pseudobonds, 973 residues, 6 models selected

select subtract #10

3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected

select subtract #9

112 atoms, 112 bonds, 11 residues, 2 models selected

hide #3 models

hide #!9 models

3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected

7552 atoms, 7744 bonds, 22 pseudobonds, 973 residues, 6 models selected

color sel & #!10 byhetero

show #!9 models

color sel & #!9-10 byhetero

hide #!9 models

show #!9 models

hide #!9 models

show #!9 models

hide #!9 models

show #!5 models

hide #!5 models

select subtract #9

3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected

show #!9 models

select subtract #10

112 atoms, 112 bonds, 11 residues, 2 models selected

hide #!10 models

show #3 models

3735 atoms, 3828 bonds, 481 residues, 2 models selected

58 atoms, 58 bonds, 4 residues, 1 model selected

hide #3 models

show #!4 models

show #!5 models

hide #!5 models

hide #!4 models

show #!6 models

hide #!6 models

show #3 models

Named views: All_H2ases, PsaC_interface, coulSide, session-start, viewH2ase, viewH2aseHbonds, zoom1, zoom2

view zoom1

view zoom2

select #9:392-393

15 atoms, 14 bonds, 2 residues, 1 model selected

show sel atoms

style sel sphere

Changed 15 atom styles

style sel stick

Changed 15 atom styles

ui tool show "Selection Inspector"

setattr sel r ribbon_hide_backbone false

Assigning ribbon_hide_backbone attribute to 2 items

style sel sphere

Changed 15 atom styles

style sel ball

Changed 15 atom styles

style sel stick

Changed 15 atom styles

ui tool show "Color Actions"

color sel lime target cspf

hide #3 models

view name linkerZoom

show #!6 models

select #6/B:392

14 atoms, 14 bonds, 1 residue, 1 model selected

select #6/B:392-398

123 atoms, 123 bonds, 7 residues, 1 model selected

ui tool show "Color Actions"

color sel lime target cspf

select #9:392-393

15 atoms, 14 bonds, 2 residues, 1 model selected

show #!7 models

select #7/A:391

16 atoms, 15 bonds, 1 residue, 1 model selected

select #7/A:391-398

134 atoms, 134 bonds, 8 residues, 1 model selected

select #7/A:397-398

37 atoms, 36 bonds, 2 residues, 1 model selected

select #7/A:391-398

134 atoms, 134 bonds, 8 residues, 1 model selected

select #7/A:399-400

28 atoms, 27 bonds, 2 residues, 1 model selected

select #7/A:391-400

162 atoms, 162 bonds, 10 residues, 1 model selected

color sel lime target cspf

show #!8 models

select #8/A:390

24 atoms, 23 bonds, 1 residue, 1 model selected

select #8/A:390-400

194 atoms, 195 bonds, 11 residues, 1 model selected

select #8/A:390

24 atoms, 23 bonds, 1 residue, 1 model selected

select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402

469 atoms, 470 bonds, 43 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556

select #3/A:399 #9/A:399 #10/A:399

24 atoms, 21 bonds, 3 residues, 3 models selected

select #3/A:399-400 #9/A:399-400 #10/A:399-400

57 atoms, 54 bonds, 6 residues, 3 models selected
MatchMaker Alignment [ID: 6] region chain A [402-403] RMSD: 34.950

select #8/A:390

24 atoms, 23 bonds, 1 residue, 1 model selected

select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402

469 atoms, 470 bonds, 43 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556

select #8/A:390

24 atoms, 23 bonds, 1 residue, 1 model selected

select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402

469 atoms, 470 bonds, 43 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556

select #8/A:390

24 atoms, 23 bonds, 1 residue, 1 model selected

select #8/A:390-400

194 atoms, 195 bonds, 11 residues, 1 model selected

select #8:390-399

344 atoms, 346 bonds, 20 residues, 1 model selected

hide #!6 models

hide #!7 models

select #8:390-402

440 atoms, 442 bonds, 26 residues, 1 model selected

color sel lime target cspf

select #3/A:392 #9/A:392 #10/A:392

21 atoms, 18 bonds, 3 residues, 3 models selected

select #3/A:392-393 #9/A:392-393 #10/A:392-393 #8/A:395-396

78 atoms, 74 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [395-396] RMSD: 30.689

select #8/A:392

22 atoms, 21 bonds, 1 residue, 1 model selected

select #8/A:392-396

88 atoms, 88 bonds, 5 residues, 1 model selected

rename #10 id 11

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif"

Chain information for HydAB_PSI_Interface_model.cif #10
Chain	Description
A	.

No chain in structure corresponds to chain ID given in local score info (chain 'B')

Associated HydAB_PSI_Interface_model.cif chain A to chain F with 0 mismatches
[Repeated 1 time(s)]Computing secondary structure

rename #10 HydAB_PSI_Interface_model_MSA.cif

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif"

Chain information for HydAB_PSI_Interface_model.cif #12
Chain	Description
A	.

No chain in structure corresponds to chain ID given in local score info (chain 'B')

Associated HydAB_PSI_Interface_model.cif chain A to chain F with 0 mismatches
[Repeated 1 time(s)]Computing secondary structure

hide #!12 models

show #!12 models

ui tool show "AlphaFold Error Plot"

alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"

Structure HydAB_PSI_Interface_model_MSA.cif #10 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms

This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.

alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"

alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json"

JSON file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json" is not AlphaFold predicted aligned error data, expected a top level list

alphafold pae #12 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"

Structure HydAB_PSI_Interface_model.cif #12 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms

This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.

ui tool show Matchmaker

matchmaker #!10,12 to #9

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker HydAB_TD_linker_model_MSA.cif, chain A (#9) with HydAB_PSI_Interface_model_MSA.cif, chain A (#10), sequence alignment score = 2279.9
RMSD between 455 pruned atom pairs is 0.339 angstroms; (across all 470 pairs: 1.307)

Matchmaker HydAB_TD_linker_model_MSA.cif, chain A (#9) with HydAB_PSI_Interface_model.cif, chain A (#12), sequence alignment score = 1931.8
RMSD between 100 pruned atom pairs is 0.836 angstroms; (across all 470 pairs: 23.291)

hide #!12 models

show #3 models

hide #3 models

hide #!8 models

hide #!9 models

select #10:cys

36 atoms, 30 bonds, 6 residues, 1 model selected

select #10:cys,unk

84 atoms, 67 bonds, 18 residues, 1 model selected

show sel atoms

select #10:unk

48 atoms, 36 bonds, 12 residues, 1 model selected

color sel orange

color sel yellow

save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs"

——— End of log from Wed Nov 5 11:09:20 2025 ———

view name session-start

opened ChimeraX session

hide #!10 models

show #!9 models

show #!8 models

show #!4 models

hide #!4 models

show #!6 models

hide #!6 models

show #!7 models

rename #12 id 16

rename #11 id 15

rename #10 id 14

rename #9 id 11

open 8ryh

Summary of feedback from opening 8ryh fetched from pdb
warning	Atom HS2 is not in the residue template for 402 /A:504

8ryh title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica [more info...]

Chain information for 8ryh #9
Chain	Description	UniProt
A	Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit	PHFL_DESVH 1-389, PHFS_DESVH 403-480

Non-standard residues in 8ryh #9
402 — dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
SF4 — iron/sulfur cluster

41 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.
Associated 8ryh chain A to chain L with 30 mismatches
Associated 8ryh chain A to chain A with 7 mismatches

rename #9 "DdHydAB_L4 8ryh"

ui tool show Matchmaker

matchmaker #!9 to #8

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHydAB_L3 9gbu, chain A (#8) with DdHydAB_L4 8ryh, chain A (#9), sequence alignment score = 2520.8
RMSD between 468 pruned atom pairs is 0.433 angstroms; (across all 469 pairs: 0.443)

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_model.cif"

Chain information for hHydAB_L4_linker_PDB_8ryh_model.cif #10
Chain	Description
A	.

No chain in structure corresponds to chain ID given in local score info (chain 'B')

Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain L with 30 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain A with 7 mismatches
Computing secondary structure

ui tool show "AlphaFold Error Plot"

hide #!11 models

show #!11 models

hide #!11 models

show #!11 models

hide #!11 models

show #!11 models

rename #3 id 13

rename #11 id 3

rename #3 id 11

rename #5 id #3

show #!2 models

hide #!11 models

hide #!10 models

hide #!9 models

hide #!8 models

hide #!7 models

show #!14 models

hide #!2.7 models

hide #2.6.1 models

show #2.6.1 models

rename #2 DdHyd_PSI_interface_opt

rename #4 id #5

rename #11 id #4

show #!4 models

hide #!4 models

show #!5 models

show #!4 models

hide #!4 models

hide #!5 models

hide #!14 models

select #2:2152-2156

65 atoms, 65 bonds, 5 residues, 1 model selected

ui tool show "Color Actions"

color sel lime target cspf

show #!5 models

show #!4 models

hide #!2 models

hide #!4 models

show #!3 models

hide #!3 models

show #!3 models

show #!6 models

show #!7 models

show #!8 models

show #!9 models

select add #5

7032 atoms, 6379 bonds, 14 pseudobonds, 1600 residues, 5 models selected

color sel light salmon

color sel gainsboro

color sel plum

color sel & #!5 byhetero

hide #!6 models

hide #!7 models

hide #!8 models

hide #!9 models

hide #!3 models

show #!4 models

select #5:391-392

30 atoms, 28 bonds, 4 residues, 1 model selected

color sel lime

show sel atoms

color sel plum target aspf

color sel byhetero

show #!6 models

show #!7 models

show #!8 models

show #!9 models

show #!2 models

hide #!2 models

hide #!8 models

hide #!7 models

hide #!6 models

hide #!5 models

hide #!4 models

show #!10 models

hide #!10 models

show #!10 models

hide #!10 models

show #!10 models

hide #!9 models

show #!9 models

alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_confidences.json"

color bfactor #10 palette alphafold

3825 atoms, 494 residues, atom bfactor range 17.3 to 99

ui tool show Matchmaker

matchmaker #!10 to #9

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHydAB_L4 8ryh, chain A (#9) with hHydAB_L4_linker_PDB_8ryh_model.cif, chain A (#10), sequence alignment score = 2532.7
RMSD between 468 pruned atom pairs is 0.400 angstroms; (across all 469 pairs: 0.426)

3855 atoms, 3954 bonds, 11 pseudobonds, 498 residues, 3 models selected

color sel & #!10 byhetero

select subtract #10

30 atoms, 28 bonds, 4 residues, 1 model selected

show #!5 models

hide #!5 models

show #!4 models

hide #!9 models

show #!9 models

hide #!9 models

show #!9 models

hide #!10 models

hide #!4 models

ui tool show "Show Sequence Viewer"

sequence chain #9/A #10/A

Alignment identifier is 1

select #9/A:402 #10/A:402

15 atoms, 13 bonds, 2 residues, 2 models selected

select #9/A:386-402 #10/A:386-402

270 atoms, 270 bonds, 1 pseudobond, 27 residues, 3 models selected
Periplasmic [Fe] Hydrogenase Large subunit,Periplasmic [Fe] Hydrogenase Small Subunit [ID: 1] region 2 chains [386-402] RMSD: 1.363

select #9/A:390 #10/A:390

35 atoms, 33 bonds, 2 residues, 2 models selected

select #9/A:390-402 #10/A:390-402

201 atoms, 199 bonds, 1 pseudobond, 19 residues, 3 models selected
Periplasmic [Fe] Hydrogenase Large subunit,Periplasmic [Fe] Hydrogenase Small Subunit [ID: 1] region 2 chains [390-402] RMSD: 1.756

color sel lime target cspf

show #!10 models

select #10:390-402

102 atoms, 102 bonds, 13 residues, 1 model selected

hide #!9 models

show #!16 models

hide #!16 models

show #!14 models

hide #!10 models

show #!10 models

show #!4 models

hide #!10 models

show #!10 models

show #!8 models

hide #!14 models

show #!7 models

show #!6 models

show #!5 models

hide #!5 models

save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs"

toolshed show

Alignment identifier is 1.1/A
Alignment identifier is 1.1/B
Alignment identifier is 1.1/C
Alignment identifier is 1.1/D
Alignment identifier is 1.1/E
Alignment identifier is 2.6/F
Alignment identifier is 6/B
Alignment identifier is 7/A
Alignment identifier is 3
Alignment identifier is 5
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11

help help:user

sequence align 16,4,5,6,7,8,9

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align #16/A,#4-9/A

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align /A

Alignment identifier is 1
Associated DdHyd_PSI.opt.chains no DdHyd (1.1) chain A to #1.1/A with 0 mismatches
Associated DdHyd_PSI.opt.chains (2.6) chain F to #16/A with 12 mismatches
Associated DdHydAB_L2 9gnk chain A to #7/A with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to #8/A with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to #8/A with 0 mismatches
Associated HydAB_PSI_Interface_model.cif chain A to #16/A with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to #15/A with 0 mismatches
Associated HydAB_PSI_Interface_model_MSA.cif chain A to #16/A with 0 mismatches
Associated DdHydAB_L4 8ryh chain A to #10/A with 0 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to #10/A with 0 mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to #15/A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to #4/A with 25 mismatches
Associated DdHydAHydB 1hfe chain M to #4/A with 25 mismatches
Associated CrHydA1 3lx4 chain A to #5/A with 0 mismatches
Associated CrHydA1 3lx4 chain B to #5/A with 0 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to #4/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Webservices job id: NZ6M9RRWIFCG5ZGZ
Webservices job finished: NZ6M9RRWIFCG5ZGZ

Populating font family aliases took 225 ms. Replace uses of missing font family "Times" with one that exists to avoid this cost.

help help:user

select add #4

3720 atoms, 3816 bonds, 11 pseudobonds, 481 residues, 2 models selected

select add #6

11777 atoms, 11489 bonds, 36 pseudobonds, 1453 residues, 4 models selected

select add #7

19934 atoms, 19195 bonds, 60 pseudobonds, 2493 residues, 6 models selected

35077 atoms, 34307 bonds, 108 pseudobonds, 3686 residues, 8 models selected

38902 atoms, 38233 bonds, 119 pseudobonds, 4180 residues, 10 models selected
Alignment identifier is 6/B
Alignment identifier is 7/A
Alignment identifier is 1
Alignment identifier is 10/A
Alignment identifier is 4/A

Alignment identifier is 4/A

select #4/D:1@FE3

1 atom, 1 residue, 1 model selected

cofr sel

Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A

sequence chain #4-5/A

Chains must have same sequence

sequence chain #4/A#5/A

Chains must have same sequence

sequence chain #4/A #5/A

Chains must have same sequence

Alignment identifier is 4/A

sequence chain #6/A

Chains must have same sequence

sequence chain #6/B

Alignment identifier is 6/B

sequence chain #7/A

Alignment identifier is 7/A

sequence chain #8/A

Alignment identifier is 8/A

sequence chain #10/A

Alignment identifier is 10/A

sequence chain #16/A

Alignment identifier is 16/A

sequence align id:4/A,id:6/b,id:7/A,id:8/A,id:10/A,id:16/A

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align id:4/A id:6/b id:7/A id:8/A id:10/A id:16/A

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align ID:4/A ID:6/B ID:7/A ID:8/A ID:10/A ID:16/A

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align ID:4

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align 4

Must specify 2 or more protein sequences

sequence align 4,6

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align 4 6

Expected a keyword

sequence align 4,6

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align ID:4,ID:6

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align [ID:4],[ID:6]

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align [ID:4/A],[ID:6/B]

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align [ID: 4/A],[ID: 6/B]

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align ID: 4/A,ID: 6/B

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align ID: 4, ID: 6

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align ID:4, ID:6

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

open /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta

Summary of feedback from opening /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta

notes

Alignment identifier is rcsb_pdb_8RYH.fasta
Associated DdHydAB_L3 9gbu chain A to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 7 mismatches
Associated DdHydAB_L3 9gbu chain B to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 7 mismatches
Associated DdHydAB_L4 8ryh chain A to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 0 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 0 mismatches
Associated DdHydAHydB 1hfe chain L to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 30 mismatches
Associated DdHydAHydB 1hfe chain M to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 30 mismatches

Opened 1 sequence from rcsb_pdb_8RYH.fasta

sequence align 4/A,6/B

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align 4,6

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align 4/A , 6/A

Expected a keyword

sequence align 4/A 6/A

Expected a keyword

sequence align 4/A

Must specify 2 or more protein sequences

sequence align 4/A,6/B

Missing or invalid "seqSource" argument: Expected alignment-id or sequences

sequence align 4/A:1,6/B:1

Alignment identifier is 1
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to chain A with 0 mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to chain A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to chain A with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain A with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Webservices job id: EQFV5H4VRVP51OI6
Webservices job finished: EQFV5H4VRVP51OI6

sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 16/A:1,4/A:1,6/B:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 16/A:1,4/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 4/A:1,6/B:1,7/A:1,8/A:1,10/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 4/A:1,6/B:1

Alignment identifier is 1
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to chain A with 0 mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to chain A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to chain A with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain A with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Webservices job id: 2Z7P362WBNIJOMWR
Webservices job finished: 2Z7P362WBNIJOMWR

sequence align 7/A:1,8/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

align4/A:1,8/A:1

Unknown command: sequence align4/A:1,8/A:1

sequence align 4/A:1,8/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 4/A:1,7/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 4/A:1,7/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence align 6/B:1,7/A:1

Alignment identifier is 1
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated DdHydAB_L2 9gnk chain A to chain A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to chain B with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain B with 25 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Webservices job id: 8ZTRX39PHNG45CRR
Webservices job finished: 8ZTRX39PHNG45CRR

sequence align 6/B:1,8/A:1

Alignment identifier is 3
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to chain A with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to chain A with 0 mismatches
Associated DdHydAB_L4 8ryh chain A to chain A with 7 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain A with 7 mismatches
Associated DdHydAHydB 1hfe chain L to chain B with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain B with 25 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 3
Webservices job id: 8ICR98YVWHUEM7RR
Webservices job finished: 8ICR98YVWHUEM7RR

sequence align 7/A:1,8/A:1

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
    input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
    renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
                                                                             ^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'

AttributeError: 'StructureSeq' object has no attribute 'atomspec'

File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"
^^^^^^^^^^^^

See log for complete Python traceback.

sequence rename "6/B:chain B" DdHydAB_L1

sequence rename "4/A:chain A" DdHydAB_TD

sequence rename "7/A:chain A" DdHydAB_L2

sequence rename "10/A:chain A" DdHydAB_L3

sequence rename 10/A:DdHydAB_L3 DdHydAB_L4

sequence rename "8/A:chain A" DdHydAB_L3

sequence rename "16/A:chain A" DdHydAB_PSI_Interface

sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1

Alignment identifier is 1
Associated DdHyd_PSI.opt.chains (2.6) chain F to DdHydAB_PSI_Interface with 12 mismatches
Associated DdHydAB_L1 8ru6 chain B to DdHydAB_L1 with 0 mismatches
Associated DdHydAB_L2 9gnk chain A to DdHydAB_L2 with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to DdHydAB_L3 with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to DdHydAB_L3 with 0 mismatches
Associated HydAB_PSI_Interface_model.cif chain A to DdHydAB_PSI_Interface with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to DdHydAB_TD with 0 mismatches
Associated HydAB_PSI_Interface_model_MSA.cif chain A to DdHydAB_PSI_Interface with 0 mismatches
Associated DdHydAB_L4 8ryh chain A to DdHydAB_L4 with 0 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to DdHydAB_L4 with 0 mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to DdHydAB_TD with 0 mismatches
Associated DdHydAHydB 1hfe chain L to DdHydAB_TD with 25 mismatches
Associated DdHydAHydB 1hfe chain M to DdHydAB_TD with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to DdHydAB_TD with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 1
Webservices job id: F9UBN2MFBD72KX6R
Webservices job finished: F9UBN2MFBD72KX6R

save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs"

ui tool show "Model Panel"

show #!5 models

hide #!6 models

hide #!7 models

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hide #!10 models

show #!10 models

hide #!10 models

show #!10 models

hide #!10 models

show #!8 models

show #!10 models

open 4xdc

4xdc title:
Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor [more info...]

Chain information for 4xdc #11
Chain	Description	UniProt
A B	Iron hydrogenase 1	PHF1_CLOPA 1-574

Non-standard residues in 4xdc #11
402 — dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
FES — FE2/S2 (inorganic) cluster
MG — magnesium ion
SF4 — iron/sulfur cluster

4xdc mmCIF Assemblies
1	author_and_software_defined_assembly
2	author_and_software_defined_assembly

63 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command.

rename #11 id 12

rename #10 id 11

rename #9 id 10

rename #8 id 9

rename #7 id 8

rename #6 id 7

rename #12 id 6

ui tool show Matchmaker

matchmaker #6/A to #5/A pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker CrHydA1 3lx4, chain A (#5) with 4xdc, chain A (#6), sequence alignment score = 892.2
RMSD between 262 pruned atom pairs is 1.077 angstroms; (across all 362 pairs: 3.983)

select #6/B

9582 atoms, 9080 bonds, 40 pseudobonds, 1170 residues, 2 models selected

hide sel cartoons

hide sel atoms

hide #!6 models

show #!6 models

select #6/A:139-207

1016 atoms, 1019 bonds, 69 residues, 1 model selected

hide #!9 models

hide #!6 models

show #!6 models

hide #!5 models

hide #!4 models

hide #!11 models

ui tool show "Color Actions"

color sel light steel blue

color sel steel blue

color sel slate gray

color sel light slate gray

color sel sky blue

color sel light sky blue

[Repeated 1 time(s)]

color sel sky blue

color sel light blue

[Repeated 1 time(s)]

select #6/A:1-138

2183 atoms, 2194 bonds, 138 residues, 1 model selected

color sel light gray

color sel silver

color sel powder blue

color sel silver

select #6/A

9693 atoms, 9132 bonds, 49 pseudobonds, 1233 residues, 2 models selected

color sel byhetero

show #!4 models

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show #!1 models

hide #1.1.4 models

hide #1.1.5 models

show #!4 models

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hide #!1 models

select #2:SF4

32 atoms, 12 bonds, 54 pseudobonds, 4 residues, 3 models selected

style sel & #!2.6 stick

Changed 24 atom styles

style sel & #!2.6 ball

Changed 24 atom styles

style sel & #!2.6 sphere

Changed 24 atom styles

style sel & #!2.6 ball

Changed 24 atom styles

hide #!6 models

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hide #!1 models

hide #!1.1 models

show #!1.1 models

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select #6/A:19-26 :<4.5 & #6/A:513-520

51 atoms, 50 bonds, 3 residues, 1 model selected

show sel atoms

style sel sphere

Changed 51 atom styles

select #6/A:513-520 :<4.5 & #6/A:19-26

46 atoms, 44 bonds, 2 residues, 1 model selected

show sel atoms

style sel sphere

Changed 46 atom styles

save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs"

open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_model.cif"

Chain information for hydab_psi_interface_model.cif #12
Chain	Description
A	.

No chain in structure corresponds to chain ID given in local score info (chain 'B')

Associated hydab_psi_interface_model.cif chain A to chain F with 12 mismatches
Associated hydab_psi_interface_model.cif chain A to DdHydAB_PSI_Interface with 12 mismatches
Computing secondary structure

hide #!12 models

show #!12 models

show #!16 models

hide #!16 models

ui tool show Log

ui tool show Matchmaker

matchmaker #12/A to #2.6/F pairing ss

Parameters

Chain pairing

Alignment algorithm

Needleman-Wunsch

Similarity matrix

BLOSUM-62

SS fraction

0.3

Gap open (HH/SS/other)

18/18/6

Gap extend

SS matrix

	H	S	O
H	6	-9	-6
S		6	-6
O			4

Iteration cutoff

Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with hydab_psi_interface_model.cif, chain A (#12), sequence alignment score = 2357.4
RMSD between 459 pruned atom pairs is 0.458 angstroms; (across all 473 pairs: 1.168)

show #!2 models

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ui tool show "AlphaFold Error Plot"

alphafold pae #12 file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_confidences.json"

color bfactor #12 palette alphafold

3658 atoms, 477 residues, atom bfactor range 24.2 to 99

close #16

ui tool show "Show Sequence Viewer"

sequence chain #12/A

Alignment identifier is 12/A

sequence align 12/A:1,1:2,1:3,1:4,1:5,1:6

Alignment identifier is 3
Associated DdHyd_PSI.opt.chains (2.6) chain F to chain A with 12 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to DdHydAB_TD with 0 mismatches
Associated HydAB_PSI_Interface_model_MSA.cif chain A to chain A with 0 mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to DdHydAB_TD with 0 mismatches
Associated DdHydAHydB 1hfe chain L to DdHydAB_TD with 25 mismatches
Associated DdHydAHydB 1hfe chain M to DdHydAB_TD with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to DdHydAB_TD with 0 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to DdHydAB_L4 with 0 mismatches
Associated DdHydAB_L4 8ryh chain A to DdHydAB_L4 with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to DdHydAB_L3 with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to DdHydAB_L3 with 0 mismatches
Associated DdHydAB_L2 9gnk chain A to DdHydAB_L2 with 0 mismatches
Associated DdHydAB_L1 8ru6 chain B to DdHydAB_L1 with 0 mismatches
Associated hydab_psi_interface_model.cif chain A to chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for alignment 3
Webservices job id: 6XMP5FXUI3IT234Y
Webservices job finished: 6XMP5FXUI3IT234Y

select #2.6/F:1796 #14/A:31 #12/A:31

20 atoms, 17 bonds, 3 residues, 3 models selected

select #2.6/F:1796 #14/A:31 #12/A:31

20 atoms, 17 bonds, 3 residues, 3 models selected
Clustal Omega Alignment [ID: 3] region chain A [35] RMSD: 0.945

sequence rename "3:chain A" DdHydAB_PSI_interface

sequence disassociate #3/L 3

Disassociated DdHydAHydB 1hfe chain L from DdHydAB_TD

sequence disassociate #3/M 3

Disassociated DdHydAHydB 1hfe chain M from DdHydAB_TD

sequence disassociate #2.6/F 3

Disassociated DdHyd_PSI.opt.chains (2.6) chain F from DdHydAB_PSI_interface

sequence associate #2.6/F 3

Associated DdHyd_PSI.opt.chains (2.6) chain F to DdHydAB_PSI_interface with 12 mismatches

sequence disassociate #2.6/F 3

Disassociated DdHyd_PSI.opt.chains (2.6) chain F from DdHydAB_PSI_interface

select #14/A:31,34,37,41,65,68,71,75,178,233,377,381 #12/A:31,34,37,41,65,68,71,75,178,233,377,381

120 atoms, 96 bonds, 24 residues, 2 models selected

select #12

3658 atoms, 3754 bonds, 11 pseudobonds, 477 residues, 2 models selected

color sel byhetero