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Changes between Initial Version and Version 1 of Ticket #14805

Timestamp:: Mar 22, 2024, 11:26:55 AM (19 months ago)
Author:: Eric Pettersen
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #14805
- Property Component Unassigned → Graphics
- Property Owner set to Tom Goddard
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Graphics hardware encountered an error and was reset

Ticket #14805 – Description

-              initial
+              v1
 atoms, 38 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum
+> color sel byhetero
+> select add #1
+atoms, 14137 bonds, 2 pseudobonds, 1846 residues, 3 models selected
+> select #2/A:340
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/B:463
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/A:744@O
+atom, 1 residue, 1 model selected
+> select #1/B:423
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+Drag select of 5 residues, 1 bonds
+> select #1/B:394
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/B
+Alignment identifier is 1/B
+> select #1/B:338
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/B:338
+atoms, 10 bonds, 1 residue, 1 model selected
+Drag select of 1 atoms, 1 bonds
+> select #1/B:338
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/B:338
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> view
+> hide sel atoms
+Drag select of 17 residues
+Drag select of 1 residues
+> hide sel atoms
+> hide sel cartoons
+Drag select of 7 residues
+> hide sel atoms
+> hide sel cartoons
+> ui tool show "Side View"
+> select #1/B:323-324
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #1/B:323-324
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #1/B:323
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #1/B:323
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #1/B:321
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:321-325
+atoms, 33 bonds, 5 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select #1/B:334-335
+atoms, 12 bonds, 2 residues, 1 model selected
+> select #1/B:334-345
+atoms, 89 bonds, 12 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select #1/B:329
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:326
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #1/B:326-332
+atoms, 52 bonds, 7 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select #1/B:126-145
+atoms, 165 bonds, 20 residues, 1 model selected
+> select #1/B:126-145
+atoms, 165 bonds, 20 residues, 1 model selected
+> select #1/B:287
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #1/B:287
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #1/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> select #1/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> show sel cartoons
+Drag select of 2 residues
+> select #1/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> select #1/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> hide sel cartoons
+> ui mousemode right distance
+> distance #2/A:501@C21 #2/A:303@NE2
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 C21 and HIS 303 NE2:
+.544Å
+> ~distance #2/A:501@C21 #2/A:303@NE2
+> ui mousemode right translate
+> ui mousemode right distance
+> distance #2/A:303@NE2 #2/A:501@O33
+Distance between 3i8p FabF platensimycin.pdb #2/A HIS 303 NE2 and 840 501 O33:
+.316Å
+> ~distance #2/A:303@NE2 #2/A:501@O33
+> distance #2/A:501@O33 #1/B:423@NE2
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O33 and PKS13-dimer-
+fit172-coot.pdb #1/B HIS 423 NE2: 2.928Å
+> distance #1/B:423@NE2 #1/B:463@NE2
+Distance between PKS13-dimer-fit172-coot.pdb #1/B HIS 423 NE2 and HIS 463 NE2:
+.792Å
+> distance #1/B:463@NE2 #2/A:501@O33
+Distance between PKS13-dimer-fit172-coot.pdb #1/B HIS 463 NE2 and 3i8p FabF
+platensimycin.pdb #2/A 840 501 O33: 3.128Å
+> ~distance #1/B:423@NE2 #1/B:463@NE2
+> distance #2/A:501@O33 #1/B:530@CD2
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O33 and PKS13-dimer-
+fit172-coot.pdb #1/B PHE 530 CD2: 6.925Å
+> ~distance #2/A:501@O33 #1/B:530@CD2
+> ui mousemode right select
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 6 atom styles
+> show sel atoms
+> hide sel cartoons
+> select #2/A:272
+atoms, 7 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 7 atom styles
+> style sel stick
+Changed 7 atom styles
+> hide sel cartoons
+> style sel stick
+Changed 7 atom styles
+> show sel atoms
+Drag select of 4 residues
+Drag select of 1 atoms, 6 residues, 1 bonds
+Drag select of 13 residues
+Drag select of 3 residues
+> ui mousemode right translate
+> ui mousemode right "translate selected models"
+> view matrix models
+> #1,1,0,0,10.381,0,1,0,-7.5023,0,0,1,-14.321,#2,-0.37428,-0.23973,0.89579,177.19,0.25984,0.9002,0.34948,135.59,-0.89017,0.36356,-0.27464,154.91
+> ui mousemode right distance
+> distance #2/A:270@OG1 #2/A:501@N28
+Distance between 3i8p FabF platensimycin.pdb #2/A THR 270 OG1 and 840 501 N28:
+.846Å
+> ~distance #2/A:270@OG1 #2/A:501@N28
+> distance #2/A:501@N28 #2/A:270@OG1
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 N28 and THR 270 OG1:
+.846Å
+> ~distance #2/A:501@N28 #2/A:270@OG1
+> distance #2/A:270@OG1 #2/A:400@CZ
+Distance between 3i8p FabF platensimycin.pdb #2/A THR 270 OG1 and PHE 400 CZ:
+.399Å
+> ui mousemode right "translate selected models"
+> ui mousemode right distance
+> distance #2/A:206@NH1 #2/A:206@NH2
+Distance between 3i8p FabF platensimycin.pdb #2/A ARG 206 NH1 and NH2: 2.300Å
+> ~distance #2/A:206@NH1 #2/A:206@NH2
+> distance #2/A:206@NH2 #2/A:501@O34
+Distance between 3i8p FabF platensimycin.pdb #2/A ARG 206 NH2 and 840 501 O34:
+.271Å
+> ~distance #2/A:206@NH2 #2/A:501@O34
+> ~distance #2/A:270@OG1 #2/A:400@CZ
+> ui mousemode right translate
+> ui mousemode right distance
+> distance #2/A:501@O34 #2/A:271@N
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O34 and SER 271 N:
+.198Å
+> distance #2/A:271@N #2/A:501@O30
+Distance between 3i8p FabF platensimycin.pdb #2/A SER 271 N and 840 501 O30:
+.486Å
+> ~distance #2/A:501@O34 #2/A:271@N
+> distance #2/A:501@O30 #2/A:206@NH1
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O30 and ARG 206 NH1:
+.741Å
+> distance #2/A:206@NH1 #2/A:501@O34
+Distance between 3i8p FabF platensimycin.pdb #2/A ARG 206 NH1 and 840 501 O34:
+.006Å
+> ~distance #2/A:501@O30 #2/A:206@NH1
+> ~distance #2/A:206@NH1 #2/A:501@O34
+> ui mousemode right select
+> select #2/A:206@CA
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> hide sel atoms
+> select #2/A:206
+atoms, 10 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:308
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/A:501@O19
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> distance #2/A:501@O34 #2/A:501@O19
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O34 and O19: 6.133Å
+> ~distance #2/A:501@O34 #2/A:501@O19
+> ui tool show Matchmaker
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 3i8p FabF
+platensimycin.pdb, chain A (#2), sequence alignment score = 654.7
+RMSD between 260 pruned atom pairs is 1.117 angstroms; (across all 400 pairs:
+.670)
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 3i8p FabF
+platensimycin.pdb, chain A (#2), sequence alignment score = 654.7
+RMSD between 260 pruned atom pairs is 1.117 angstroms; (across all 400 pairs:
+.670)
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 3i8p FabF
+platensimycin.pdb, chain A (#2), sequence alignment score = 654.7
+RMSD between 260 pruned atom pairs is 1.117 angstroms; (across all 400 pairs:
+.670)
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 3i8p FabF
+platensimycin.pdb, chain A (#2), sequence alignment score = 654.7
+RMSD between 260 pruned atom pairs is 1.117 angstroms; (across all 400 pairs:
+.670)
+> ui mousemode right select
+> select #2/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> style sel stick
+Changed 5 atom styles
+> show sel atoms
+> hide sel cartoons
+> show sel atoms
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,-0.37428,-0.23973,0.89579,169.32,0.25984,0.9002,0.34948,144.04,-0.89017,0.36356,-0.27464,150.42
+> undo
+> ui mousemode right translate
+> ui mousemode right distance
+> distance #2/A:501@O19 #2/A:309@N
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O19 and ALA 309 N:
+.004Å
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> ui mousemode right "translate selected models"
+> ui mousemode right select
+> ui mousemode right distance
+> distance #2/A:309@N #2/A:501@O20
+Distance between 3i8p FabF platensimycin.pdb #2/A ALA 309 N and 840 501 O20:
+.422Å
+> ~distance #2/A:309@N #2/A:501@O20
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select clear
+Drag select of 2 residues
+> ui mousemode right translate
+> ui mousemode right select
+> select #1/B:393
+atoms, 4 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> ui mousemode right distance
+> distance #2/A:501@O20 #1/B:393@N
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O20 and PKS13-dimer-
+fit172-coot.pdb #1/B ALA 393 N: 6.993Å
+> distance #1/B:393@N #2/A:501@O30
+Distance between PKS13-dimer-fit172-coot.pdb #1/B ALA 393 N and 3i8p FabF
+platensimycin.pdb #2/A 840 501 O30: 4.302Å
+> ~distance #2/A:501@O20 #1/B:393@N
+> ~distance #1/B:393@N #2/A:501@O30
+> ~distance #2/A:271@N #2/A:501@O30
+> ui mousemode right select
+> show sel cartoons
+> hide sel atoms
+> show sel cartoons
+> hide sel atoms
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui mousemode right translate
+> ui mousemode right distance
+> ~distance #2/A:501@O19 #2/A:309@N
+> ui tool show "Show Sequence Viewer"
+> sequence chain #2/A
+Alignment identifier is 2/A
+> select #2/A:206
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #2/A:206
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select
+> #2/A:19-29,63-68,71-89,96-98,110-129,132-138,140-151,161-180,195-205,214-219,243-249,276-291,293-297,307-328,334-339,341-360
+atoms, 1382 bonds, 191 residues, 1 model selected
+> select #2/A:163
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/A:163
+atoms, 4 bonds, 1 residue, 1 model selected
+> show sel atoms
+> ui mousemode right select
+> ui mousemode right distance
+> distance #2/A:501@O30 #2/A:400@CD1
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O30 and PHE 400 CD1:
+.794Å
+> ~distance #2/A:501@O30 #2/A:400@CD1
+> distance #2/A:400@CD1 #2/A:398@CA
+Distance between 3i8p FabF platensimycin.pdb #2/A PHE 400 CD1 and PHE 398 CA:
+.314Å
+> ~distance #2/A:400@CD1 #2/A:398@CA
+> ui mousemode right select
+> select #2/A:398
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #1/B:528@CB
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #1/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+Drag select of 8 residues
+Drag select of 12 residues
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select #2/A:163
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> ui mousemode right distance
+> distance #2/A:270@O #2/A:501@N28
+Distance between 3i8p FabF platensimycin.pdb #2/A THR 270 O and 840 501 N28:
+.837Å
+> ui mousemode right select
+> select #1/B:392
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> ui mousemode right distance
+> distance #2/A:501@N28 #1/B:392@O
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 N28 and PKS13-dimer-
+fit172-coot.pdb #1/B ILE 392 O: 3.407Å
+> ~distance #2/A:501@N28 #1/B:392@O
+> distance #1/B:392@O #2/A:501@N28
+Distance between PKS13-dimer-fit172-coot.pdb #1/B ILE 392 O and 3i8p FabF
+platensimycin.pdb #2/A 840 501 N28: 3.407Å
+> show sel cartoons
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> show sel cartoons
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> color #3 #63fac8ff models
+> color #3 #79fac4ff models
+> color #3 #5cfad2ff models
+> color #3 #32fab7ff models
+> ui mousemode right distance
+> ~distance #2/A:270@O #2/A:501@N28
+> hide sel cartoons
+> distance #2/A:501@N28 #2/A:270@O
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 N28 and THR 270 O:
+.837Å
+> show sel cartoons
+> distance #2/A:270@O #2/A:303@NE2
+Distance between 3i8p FabF platensimycin.pdb #2/A THR 270 O and HIS 303 NE2:
+.835Å
+> distance #2/A:303@NE2 #2/A:501@O33
+Distance between 3i8p FabF platensimycin.pdb #2/A HIS 303 NE2 and 840 501 O33:
+.316Å
+> ~distance #2/A:270@O #2/A:303@NE2
+> distance #2/A:501@O33 #2/A:340@NE2
+Distance between 3i8p FabF platensimycin.pdb #2/A 840 501 O33 and HIS 340 NE2:
+.753Å
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #1/B:394
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:272
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/A:272
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> hide sel atoms
+> ui mousemode right translate
+> select clear
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting shadows true
+> lighting shadows false
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting soft
+> lighting full
+> preset "initial styles" "original look"
+Using preset: Initial Styles / Original Look
+Preset implemented in Python; no expansion to individual ChimeraX commands
+available.
+> undo
+> redo
+> preset "initial styles" "original look"
+Using preset: Initial Styles / Original Look
+Preset implemented in Python; no expansion to individual ChimeraX commands
+available.
+> preset "initial styles" "original look"
+Using preset: Initial Styles / Original Look
+Preset implemented in Python; no expansion to individual ChimeraX commands
+available.
+> lighting shadows false
+> ui mousemode right select
+> select #1/B:463
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #1/B:530
+atoms, 11 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #1/B:423
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #1/B:423
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select ::name="840"
+atoms, 38 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum
+> color sel byhetero
+> select #1/B:287
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #1/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:398
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> open "/Users/sarah/Documents/Work/PKS13/7vef malonate substrate
+> analogue.pdb"
+vef malonate substrate analogue.pdb title:
+The structure of GFSA KSQ-At didomain In complex with A malonate substrate
+analog [more info...]
+Chain information for 7vef malonate substrate analogue.pdb #4
+---
+Chain | Description
+A | polyketide synthase
+Non-standard residues in 7vef malonate substrate analogue.pdb #4
+---
+IU — N-(2-acetamidoethyl)-2-nitro-ethanamide
+GOL — glycerol (glycerin; propane-1,2,3-triol)
+> color #4 #d1b58cff
+> color #1 #89cdebff
+> color #2 #d0b68cff
+> close #4
+> select ::name="840"
+atoms, 38 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum
+> select #2/A
+atoms, 3094 bonds, 3 pseudobonds, 950 residues, 2 models selected
+> color (#2 & sel) byhetero
+> select #1/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> hide sel cartoons
+> select #1/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> color (#!1 & sel) byhetero
+> select clear
+> save /Users/sarah/Desktop/image1.png supersample 3
+> hide #3.1 models
+> color #3 #fdd900ff models
+> color #3 #48fdb4ff models
+> color #3 #fbdb00ff models
+> ui tool show "Color Actions"
+> select add #3
+pseudobonds, 2 models selected
+> select subtract #3
+Nothing selected
+> select #2/A:282
+atoms, 4 bonds, 1 residue, 1 model selected
+> color #3 #52fb97ff models
+> select clear
+> ui tool show "Color Actions"
+> color sel yellow
+> ui tool show "Color Actions"
+> color sel gold
+> ui tool show "Color Actions"
+> color sel gold
+> ui tool show "Color Actions"
+> color sel gold
+> save /Users/sarah/Desktop/image2.png supersample 3
+> select clear
+> save /Users/sarah/Desktop/image3.png supersample 3
+> select #1/B:392
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> ui mousemode right select
+> select #2/A:803@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:594@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:722@O
+atom, 1 residue, 1 model selected
+> select #2/A:722@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:926@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:558@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #2/A:688@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:744@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:584@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:761@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:308
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:307
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+Drag select of 5 residues
+> select #2/A:857@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+Drag select of 2 residues
+> select clear
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/A:205
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/A:205
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel atoms
+Drag select of 4 residues, 1 bonds
+Drag select of 5 residues, 1 atoms, 1 bonds
+> select #2/A:206
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #2/A:206
+atoms, 10 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #2/A:271
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel atoms
+Drag select of 3 residues, 1 atoms
+Drag select of 4 residues
+> select clear
+> select #2/A:272-273
+atoms, 15 bonds, 2 residues, 1 model selected
+> select #2/A:272-273
+atoms, 15 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image1.png supersample 3
+> open "/Users/sarah/Documents/Work/PKS13/2gfx FabF platensimycin.pdb"
+gfx FabF platensimycin.pdb title:
+Structure of E. Coli fabf(C163Q) In complex with platensimycin [more info...]
+Chain information for 2gfx FabF platensimycin.pdb #4
+---
+Chain | Description | UniProt
+A | 3-oxoacyl-[ACYL-carrier-protein] synthase II; β-ketoacyl- ACP synthase II;
+KAS II; FABF | FABF_ECOLI 1-412
+Non-standard residues in 2gfx FabF platensimycin.pdb #4
+---
+PMN — platensimycin
+> ui tool show Matchmaker
+> matchmaker #4 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 2gfx FabF
+platensimycin.pdb, chain A (#4), sequence alignment score = 656.7
+RMSD between 261 pruned atom pairs is 1.122 angstroms; (across all 400 pairs:
+.638)
+> matchmaker #4 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 2gfx FabF
+platensimycin.pdb, chain A (#4), sequence alignment score = 656.7
+RMSD between 261 pruned atom pairs is 1.122 angstroms; (across all 400 pairs:
+.638)
+> color #3.1 #cfb78cff models
+> select ::name="840"
+atoms, 38 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum
+> select #4/A
+atoms, 3096 bonds, 522 residues, 1 model selected
+> color sel byhetero
+> color #4 #ceb88cff
+> select ::name="840"
+atoms, 38 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum
+> color sel byhetero
+> select ::name="PMN"
+atoms, 36 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum
+> color sel byhetero
+> hide #2 models
+> ui mousemode right distance
+> distance #2/A:340@NE2 #1/B:423@NE2
+Distance between 3i8p FabF platensimycin.pdb #2/A HIS 340 NE2 and PKS13-dimer-
+fit172-coot.pdb #1/B HIS 423 NE2: 3.805Å
+> distance #1/B:423@NE2 #4/A:1001@O33
+Distance between PKS13-dimer-fit172-coot.pdb #1/B HIS 423 NE2 and 2gfx FabF
+platensimycin.pdb #4/A PMN 1001 O33: 2.290Å
+> distance #4/A:1001@O33 #1/B:463@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and
+PKS13-dimer-fit172-coot.pdb #1/B HIS 463 NE2: 3.288Å
+> distance #1/B:463@NE2 #1/B:392@CB
+Distance between PKS13-dimer-fit172-coot.pdb #1/B HIS 463 NE2 and ILE 392 CB:
+.044Å
+> ~distance #1/B:463@NE2 #1/B:392@CB
+> ui mousemode right select
+> show sel atoms
+> hide sel cartoons
+> select #1/B:392@O
+atom, 1 residue, 1 model selected
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> select #4/A
+atoms, 3096 bonds, 522 residues, 1 model selected
+> color sel byhetero
+> ui mousemode right distance
+> distance #1/B:392@CB #1/B:392@O
+Distance between PKS13-dimer-fit172-coot.pdb #1/B ILE 392 CB and O: 2.862Å
+> ~distance #1/B:392@CB #1/B:392@O
+> distance #1/B:392@O #4/A:1001@N28
+Distance between PKS13-dimer-fit172-coot.pdb #1/B ILE 392 O and 2gfx FabF
+platensimycin.pdb #4/A PMN 1001 N28: 3.314Å
+> show #3.1 models
+> select clear
+> ui mousemode right select
+> select #4/A:1056@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #4/A:1072@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #4/A:1010@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/A
+Alignment identifier is 4/A
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show #4#!1 atoms
+> hide #4#!1 atoms
+> undo
+> select
+> #2/A:19-29,63-68,71-89,96-98,110-129,132-138,140-151,161-180,195-205,214-219,243-249,276-291,293-297,307-328,334-339,341-360
+atoms, 1382 bonds, 191 residues, 1 model selected
+> select #2/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show #4#!1 atoms
+> undo
+> select
+> #4/A:5-13,34-36,49-51,100-105,156-157,184-191,234-242,255-264,297-301,330-332,361-362,385-386,392-399,403-411
+atoms, 545 bonds, 79 residues, 1 model selected
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #4/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> hide sel cartoons
+> select #1/B:429
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #1/B:430
+atoms, 3 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> show sel atoms
+> hide sel cartoons
+> select #1/B:429
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> ui mousemode right distance
+> distance #4/A:1001@N28 #4/A:309@N
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 N28 and ALA 309 N:
+.132Å
+> distance #4/A:309@N #4/A:1001@O19
+Distance between 2gfx FabF platensimycin.pdb #4/A ALA 309 N and PMN 1001 O19:
+.034Å
+> ~distance #4/A:1001@N28 #4/A:309@N
+> distance #4/A:1001@O19 #1/B:429@N
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O19 and
+PKS13-dimer-fit172-coot.pdb #1/B LEU 429 N: 4.642Å
+> distance #1/B:429@N #4/A:1001@O19
+Distance already exists; modify distance properties with 'distance style'
+> distance #4/A:1001@O19 #1/B:430@N
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O19 and
+PKS13-dimer-fit172-coot.pdb #1/B GLY 430 N: 4.550Å
+> ~distance #4/A:1001@O19 #1/B:430@N
+> ~distance #4/A:1001@O19 #1/B:429@N
+> ui mousemode right translate
+> ui mousemode right select
+> select #4/A:308
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> color #3 #6cfaa5ff models
+> ui mousemode right distance
+> distance #1/B:430@N #4/A:1001@O33
+Distance between PKS13-dimer-fit172-coot.pdb #1/B GLY 430 N and 2gfx FabF
+platensimycin.pdb #4/A PMN 1001 O33: 10.703Å
+> ~distance #1/B:430@N #4/A:1001@O33
+> ~distance #2/A:340@NE2 #1/B:423@NE2
+> distance #4/A:303@NE2 #4/A:1001@O33
+Distance between 2gfx FabF platensimycin.pdb #4/A HIS 303 NE2 and PMN 1001
+O33: 2.586Å
+> distance #4/A:1001@O33 #4/A:340@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and HIS 340
+NE2: 2.829Å
+> ~distance #4/A:309@N #4/A:1001@O19
+> distance #4/A:340@NE2 #4/A:1001@O19
+Distance between 2gfx FabF platensimycin.pdb #4/A HIS 340 NE2 and PMN 1001
+O19: 11.768Å
+> ~distance #4/A:340@NE2 #4/A:1001@O19
+> distance #4/A:1001@O19 #4/A:309@N
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O19 and ALA 309 N:
+.034Å
+> distance #4/A:309@N #4/A:270@O
+Distance between 2gfx FabF platensimycin.pdb #4/A ALA 309 N and THR 270 O:
+.578Å
+> distance #4/A:270@O #4/A:1001@N28
+Distance between 2gfx FabF platensimycin.pdb #4/A THR 270 O and PMN 1001 N28:
+.908Å
+> ~distance #4/A:270@O #4/A:1001@N28
+> distance #4/A:1001@N28 #4/A:270@O
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 N28 and THR 270 O:
+.908Å
+> ~distance #4/A:309@N #4/A:270@O
+> ui mousemode right select
+> select #4/A:272
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #4/A:398
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select #4/A:270@CB
+atom, 1 residue, 1 model selected
+> select #4/A:270@C
+atom, 1 residue, 1 model selected
+> show sel cartoons
+> select #4/A:309@C
+atom, 1 residue, 1 model selected
+> show sel cartoons
+Drag select of 1 atoms, 2 residues
+> show sel cartoons
+> ui mousemode right translate
+> ui mousemode right select
+> select #4/A:307
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui mousemode right translate
+> select clear
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image1.png supersample 3
+> hide #3.1 models
+> save /Users/sarah/Desktop/image2.png supersample 3
+> save /Users/sarah/Desktop/image1.png supersample 3
+> close
+> open "/Users/sarah/Documents/Work/DprE2/DprE1_E2 cytochrome oxidase AF
+> model.pdb"
+Chain information for DprE1_E2 cytochrome oxidase AF model.pdb #1
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+> mlp
+Map values for surface "DprE1_E2 cytochrome oxidase AF model.pdb_A SES
+surface": minimum -27.17, mean -4.789, maximum 26.5
+Map values for surface "DprE1_E2 cytochrome oxidase AF model.pdb_B SES
+surface": minimum -31.07, mean -4.287, maximum 23.25
+Map values for surface "DprE1_E2 cytochrome oxidase AF model.pdb_C SES
+surface": minimum -31.43, mean 0.01913, maximum 26.63
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide surfaces
+> ui mousemode right select
+Drag select of 38 residues
+Drag select of 29 residues
+Drag select of 46 residues
+Drag select of 96 residues
+> ui tool show H-Bonds
+> hbonds sel color #00fa34 restrict both reveal true
+hydrogen bonds found
+Drag select of 19 residues
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models #1,1,0,0,-10.644,0,1,0,21.542,0,0,1,14.703
+> ui mousemode right select
+> select /B:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select /B:3
+atoms, 7 bonds, 1 residue, 1 model selected
+> select clear
+Drag select of 3 atoms, 26 residues, 1 pseudobonds, 3 bonds
+Drag select of 18 residues
+> select /B:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add /B:2
+atoms, 13 bonds, 2 residues, 2 models selected
+> select add /B:6
+atoms, 19 bonds, 3 residues, 2 models selected
+> select add /B:7
+atoms, 22 bonds, 4 residues, 2 models selected
+> select add /B:4
+atoms, 29 bonds, 5 residues, 2 models selected
+> select add /B:3
+atoms, 36 bonds, 6 residues, 2 models selected
+> select add /B:5
+atoms, 40 bonds, 7 residues, 2 models selected
+> ui tool show H-Bonds
+> hbonds sel color #00fa34 reveal true
+hydrogen bonds found
+> ui tool show Contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+contacts
+Drag select of 5 atoms, 41 residues, 5 bonds
+> select /B:237
+atoms, 6 bonds, 1 residue, 1 model selected
+Drag select of 11 atoms, 55 residues, 11 bonds
+Drag select of 8 atoms, 52 residues, 7 bonds
+> select clear
+Drag select of 1 atoms, 46 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+contacts
+> ui mousemode right zoom
+> ui mousemode right "translate selected models"
+> view matrix models #1,1,0,0,-11.472,0,1,0,14.426,0,0,1,0.28481
+> view matrix models #1,1,0,0,-5.6235,0,1,0,5.2741,0,0,1,-0.73604
+> ui mousemode right zoom
+> ui mousemode right select
+> ui mousemode right translate
+> ui mousemode right select
+Drag select of 6 residues
+Drag select of 7 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+Drag select of 3 residues
+> ui mousemode right select
+Drag select of 13 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> contacts sel resSeparation 5 interModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> contacts sel resSeparation 5 intraMol false ignoreHiddenModels true reveal
+> true
+No contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+No contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+No contacts
+> show sel atoms
+Drag select of 10 residues
+> show sel atoms
+Drag select of 8 atoms, 9 residues, 7 bonds
+Drag select of 8 atoms, 10 residues, 1 pseudobonds, 9 bonds
+> open
+> /Users/sarah/Downloads/test_e1b68_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
+Chain information for
+test_e1b68_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+Drag select of 30 residues
+> ui mousemode right translate
+> open
+> /Users/sarah/Downloads/test_e1b68_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
+Chain information for
+test_e1b68_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #3
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+> open "/Users/sarah/Documents/Work/DprE2/DprE1_E2 cytochrome oxidase AF model
+> 2.pdb"
+Chain information for DprE1_E2 cytochrome oxidase AF model 2.pdb #4
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+> hide #3 models
+> hide #2 models
+> hide #!1 models
+> ui mousemode right select
+Drag select of 31 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> ui mousemode right select
+Drag select of 6 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> open "/Users/sarah/Downloads/DprE2 dimer cytochrom C dimer.pdb"
+Chain information for DprE2 dimer cytochrom C dimer.pdb #6
+---
+Chain | Description
+A B | No description available
+C D | No description available
+> hide #5 models
+> hide #4 models
+> mlp #6
+Map values for surface "DprE2 dimer cytochrom C dimer.pdb_A SES surface":
+minimum -31.8, mean -4.429, maximum 24.22
+Map values for surface "DprE2 dimer cytochrom C dimer.pdb_B SES surface":
+minimum -32.3, mean -4.433, maximum 24.32
+Map values for surface "DprE2 dimer cytochrom C dimer.pdb_C SES surface":
+minimum -29.45, mean 0.09552, maximum 23.9
+Map values for surface "DprE2 dimer cytochrom C dimer.pdb_D SES surface":
+minimum -30.07, mean 0.1456, maximum 25.39
+To also show corresponding color key, enter the above mlp command and add key
+true
+Drag select of DprE2 dimer cytochrom C dimer.pdb_C SES surface, 3062 of 468852
+triangles, 5 residues
+> hide sel surfaces
+> select
+atoms, 54320 bonds, 59 pseudobonds, 6806 residues, 7 models selected
+> hide sel & #!6 surfaces
+> ui mousemode right select
+Drag select of 29 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> show #!1 models
+> ui tool show Matchmaker
+> matchmaker #!6 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE1_E2 cytochrome oxidase AF model.pdb, chain C (#1) with DprE2
+dimer cytochrom C dimer.pdb, chain C (#6), sequence alignment score = 3060.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> select clear
+> ui tool show Matchmaker
+> matchmaker #!6 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE1_E2 cytochrome oxidase AF model.pdb, chain C (#1) with DprE2
+dimer cytochrom C dimer.pdb, chain C (#6), sequence alignment score = 3060.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> matchmaker #!6 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE1_E2 cytochrome oxidase AF model.pdb, chain C (#1) with DprE2
+dimer cytochrom C dimer.pdb, chain C (#6), sequence alignment score = 3060.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> matchmaker #!6 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE1_E2 cytochrome oxidase AF model.pdb, chain C (#1) with DprE2
+dimer cytochrom C dimer.pdb, chain C (#6), sequence alignment score = 3060.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> matchmaker #!6 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE1_E2 cytochrome oxidase AF model.pdb, chain C (#1) with DprE2
+dimer cytochrom C dimer.pdb, chain C (#6), sequence alignment score = 3060.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> close
+> open "/Users/sarah/Downloads/DprE2 dimer cytochrom C dimer.pdb" format pdb
+Chain information for DprE2 dimer cytochrom C dimer.pdb #1
+---
+Chain | Description
+A B | No description available
+C D | No description available
+Drag select of 11 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+Drag select of 13 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+Drag select of 25 residues
+Drag select of 50 residues
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> open "/Users/sarah/Documents/Work/DprE2/DprE1_E2 cytochrome oxidase AF
+> model.pdb"
+Chain information for DprE1_E2 cytochrome oxidase AF model.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+> ui tool show Matchmaker
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE2 dimer cytochrom C dimer.pdb, chain C (#1) with DprE1_E2
+cytochrome oxidase AF model.pdb, chain C (#2), sequence alignment score =
+.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE2 dimer cytochrom C dimer.pdb, chain C (#1) with DprE1_E2
+cytochrome oxidase AF model.pdb, chain C (#2), sequence alignment score =
+.2
+RMSD between 540 pruned atom pairs is 0.342 angstroms; (across all 573 pairs:
+.937)
+> select
+atoms, 23534 bonds, 186 pseudobonds, 2942 residues, 3 models selected
+> select #1/D
+atoms, 4676 bonds, 573 residues, 1 model selected
+> ui mousemode right "translate selected models"
+> view matrix models #1,1,0,0,-53.425,0,1,0,-35.813,0,0,1,-35.053
+> select clear
+> ui mousemode right rotate
+> select
+atoms, 23534 bonds, 186 pseudobonds, 2942 residues, 3 models selected
+> hide sel atoms
+> select clear
+> ui mousemode right select
+Drag select of 31 residues
+Drag select of 35 residues
+> ui tool show Contacts
+> contacts sel restrict both resSeparation 5 intraRes true ignoreHiddenModels
+> true reveal true
+contacts
+> ui mousemode right zoom
+> ui mousemode right translate
+> ui mousemode right select
+> select #2/B:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #2/B:2
+atoms, 13 bonds, 2 residues, 1 model selected
+> select add #2/B:181
+atoms, 25 bonds, 3 residues, 1 model selected
+> select add #2/B:4
+atoms, 32 bonds, 4 residues, 1 model selected
+> select subtract #2/B:181
+atoms, 20 bonds, 3 residues, 1 model selected
+> select add #2/B:3
+atoms, 27 bonds, 4 residues, 1 model selected
+> select add #2/B:7
+atoms, 30 bonds, 5 residues, 1 model selected
+> select add #2/B:6
+atoms, 36 bonds, 6 residues, 1 model selected
+> select add #2/B:5
+atoms, 40 bonds, 7 residues, 1 model selected
+> ui tool show Contacts
+> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true reveal
+> true
+contacts
+> open "/Users/sarah/Downloads/DprE2 dimer Cyto C mon.pdb"
+Chain information for DprE2 dimer Cyto C mon.pdb #4
+---
+Chain | Description
+A B | No description available
+C | No description available
+> hide #!1 models
+> hide #!2 models
+> hide #3 models
+> view #3 clip false
+No displayed objects specified.
+> show #3 target m
+> view #3 clip false
+No displayed objects specified.
+> select add #4
+atoms, 8636 bonds, 1088 residues, 2 models selected
+> show #4 target m
+> view #4 clip false
+> select clear
+> mlp #4
+Map values for surface "DprE2 dimer Cyto C mon.pdb_A SES surface": minimum
+-31.24, mean -4.411, maximum 23.42
+Map values for surface "DprE2 dimer Cyto C mon.pdb_B SES surface": minimum
+-31.65, mean -4.357, maximum 23.47
+Map values for surface "DprE2 dimer Cyto C mon.pdb_C SES surface": minimum
+-29.95, mean 0.1403, maximum 26.04
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide #!4 surfaces
+> ui mousemode right select
+Drag select of 150 residues
+> ui tool show Contacts
+> contacts sel restrict both resSeparation 5 intraModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> contacts sel restrict both resSeparation 5 intraModel false intraMol false
+> ignoreHiddenModels true reveal true
+No contacts
+> ui tool show Contacts
+> contacts sel restrict both resSeparation 5 intraMol false ignoreHiddenModels
+> true reveal true
+contacts
+> select clear
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui mousemode right "translate selected models"
+> ui mousemode right rotate
+> ui mousemode right translate
+> ui tool show "Color Actions"
+> color bychain
+> open "/Users/sarah/Downloads/DprE2 dimer cyto C mon Ecoli.pdb"
+Chain information for DprE2 dimer cyto C mon Ecoli.pdb #5
+---
+Chain | Description
+A B | No description available
+C | No description available
+> hide #3 models
+> hide #!4 models
+> mlp #5
+Map values for surface "DprE2 dimer cyto C mon Ecoli.pdb_A SES surface":
+minimum -31.61, mean -4.417, maximum 24.52
+Map values for surface "DprE2 dimer cyto C mon Ecoli.pdb_B SES surface":
+minimum -31.38, mean -4.322, maximum 24.27
+Map values for surface "DprE2 dimer cyto C mon Ecoli.pdb_C SES surface":
+minimum -28.27, mean 0.6407, maximum 24.18
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide #!5 surfaces
+> show #!4 models
+> ui tool show Matchmaker
+> matchmaker #!5 to #4
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE2 dimer Cyto C mon.pdb, chain C (#4) with DprE2 dimer cyto C
+mon Ecoli.pdb, chain C (#5), sequence alignment score = 1539.8
+RMSD between 469 pruned atom pairs is 0.736 angstroms; (across all 551 pairs:
+.681)
+> select #4/A
+atoms, 1960 bonds, 254 residues, 1 model selected
+> select #4/B
+atoms, 1960 bonds, 254 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #!5 to #4 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE2 dimer Cyto C mon.pdb, chain B (#4) with DprE2 dimer cyto C
+mon Ecoli.pdb, chain A (#5), sequence alignment score = 1275.6
+RMSD between 253 pruned atom pairs is 0.132 angstroms; (across all 254 pairs:
+.239)
+> matchmaker #!5 to #4 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE2 dimer Cyto C mon.pdb, chain B (#4) with DprE2 dimer cyto C
+mon Ecoli.pdb, chain A (#5), sequence alignment score = 1275.6
+RMSD between 253 pruned atom pairs is 0.132 angstroms; (across all 254 pairs:
+.239)
+> select #4/C
+atoms, 4676 bonds, 573 residues, 1 model selected
+> ui tool show Matchmaker
+> matchmaker #!5 to #4 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker DprE2 dimer Cyto C mon.pdb, chain C (#4) with DprE2 dimer cyto C
+mon Ecoli.pdb, chain C (#5), sequence alignment score = 1539.8
+RMSD between 469 pruned atom pairs is 0.736 angstroms; (across all 551 pairs:
+.681)
+> select add #4
+atoms, 8596 bonds, 96 pseudobonds, 1081 residues, 3 models selected
+> color (#!4 & sel) light sea green
+> select clear
+> open "/Users/sarah/Downloads/DprE1E2 cyto C mon Ecoli.pdb"
+Chain information for DprE1E2 cyto C mon Ecoli.pdb #6
+---
+Chain | Description
+A B | No description available
+C | No description available
+> hide #!5 models
+> hide #!4 models
+> mlp #6
+Map values for surface "DprE1E2 cyto C mon Ecoli.pdb_A SES surface": minimum
+-31.61, mean -4.417, maximum 24.52
+Map values for surface "DprE1E2 cyto C mon Ecoli.pdb_B SES surface": minimum
+-31.38, mean -4.322, maximum 24.27
+Map values for surface "DprE1E2 cyto C mon Ecoli.pdb_C SES surface": minimum
+-28.27, mean 0.6407, maximum 24.18
+To also show corresponding color key, enter the above mlp command and add key
+true
+> close
+> open "/Users/sarah/Documents/Work/PKS13/2gfx FabF platensimycin.pdb" format
+> pdb
+gfx FabF platensimycin.pdb title:
+Structure of E. Coli fabf(C163Q) In complex with platensimycin [more info...]
+Chain information for 2gfx FabF platensimycin.pdb #1
+---
+Chain | Description | UniProt
+A | 3-oxoacyl-[ACYL-carrier-protein] synthase II; β-ketoacyl- ACP synthase II;
+KAS II; FABF | FABF_ECOLI 1-412
+Non-standard residues in 2gfx FabF platensimycin.pdb #1
+---
+PMN — platensimycin
+> close
+> open "/Users/sarah/Documents/Work/PKS13/2gfx FabF platensimycin.pdb" format
+> pdb
+gfx FabF platensimycin.pdb title:
+Structure of E. Coli fabf(C163Q) In complex with platensimycin [more info...]
+Chain information for 2gfx FabF platensimycin.pdb #1
+---
+Chain | Description | UniProt
+A | 3-oxoacyl-[ACYL-carrier-protein] synthase II; β-ketoacyl- ACP synthase II;
+KAS II; FABF | FABF_ECOLI 1-412
+Non-standard residues in 2gfx FabF platensimycin.pdb #1
+---
+PMN — platensimycin
+> close
+> open "/Users/sarah/Documents/Work/PKS13/Pks13 cerulenin.pdb"
+Summary of feedback from opening /Users/sarah/Documents/Work/PKS13/Pks13
+cerulenin.pdb
+---
+warning | Start residue of secondary structure not found: HELIX 1 1 CYS B 202
+CYS B 202 1 1
+Pks13 cerulenin.pdb title:
+Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide
+B synthase [more info...]
+Chain information for Pks13 cerulenin.pdb
+---
+Chain | Description | UniProt
+.2/A | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
+.2/B | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
+> close
+> open "/Users/sarah/Documents/Work/PKS13/2qo3 KS3AT3 cerulenin.pdb"
+qo3 KS3AT3 cerulenin.pdb title:
+Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide
+B synthase [more info...]
+Chain information for 2qo3 KS3AT3 cerulenin.pdb #1
+---
+Chain | Description | UniProt
+A B | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
+Non-standard residues in 2qo3 KS3AT3 cerulenin.pdb #1
+---
+ACT — acetate ion
+CER — (2S, 3R)-3-hydroxy-4-oxo-7,10-trans,trans-dodecadienamide (cerulenin)
+CL — chloride ion
+> open /Users/sarah/Documents/Work/PKS13/PKS13-dimer-fit172-coot.pdb
+Chain information for PKS13-dimer-fit172-coot.pdb #2
+---
+Chain | Description
+A | No description available
+B | No description available
+> ui tool show Matchmaker
+> matchmaker #!2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1858.5
+RMSD between 320 pruned atom pairs is 0.886 angstroms; (across all 857 pairs:
+.486)
+> matchmaker #!2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1858.5
+RMSD between 320 pruned atom pairs is 0.886 angstroms; (across all 857 pairs:
+.486)
+> ui mousemode right select
+Drag select of 33 atoms, 840 residues, 28 bonds
+> hide sel atoms
+Drag select of 4 residues
+Drag select of 41 atoms, 957 residues, 1 pseudobonds, 35 bonds
+> hide sel atoms
+> select clear
+> preset cartoons/nucleotides licorice/ovals
+Using preset: Cartoons/Nucleotides / Licorice/Ovals
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    show nucleic
+    hide protein|solvent|H
+    surf hide
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    cartoon
+    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
+    cartoon style ~(nucleic|strand) x round
+    cartoon style (nucleic|strand) x rect
+    cartoon style protein modeh default arrows f x round width 1 thick 1
+    cartoon style nucleic x round width 1.6 thick 1.6
+    nucleotides tube/slab shape ellipsoid
+> preset cartoons/nucleotides cylinders/stubs
+Using preset: Cartoons/Nucleotides / Cylinders/Stubs
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    show nucleic
+    hide protein|solvent|H
+    surf hide
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    cartoon
+    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
+    cartoon style ~(nucleic|strand) x round
+    cartoon style (nucleic|strand) x rect
+    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
+    cartoon style nucleic x round width 1.6 thick 1.6
+    nucleotides stubs
+> preset cartoons/nucleotides ribbons/slabs
+Using preset: Cartoons/Nucleotides / Ribbons/Slabs
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    show nucleic
+    hide protein|solvent|H
+    surf hide
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    cartoon
+    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
+    cartoon style ~(nucleic|strand) x round
+    cartoon style (nucleic|strand) x rect
+    nucleotides tube/slab shape box
+> coulombic
+The following residues are missing heavy (non-hydrogen) atoms, which may
+result in inaccurate electrostatics:
+PKS13-dimer-fit172-coot.pdb #2/A GLU 106
+PKS13-dimer-fit172-coot.pdb #2/A GLU 159
+PKS13-dimer-fit172-coot.pdb #2/A GLU 162
+PKS13-dimer-fit172-coot.pdb #2/A GLU 163
+PKS13-dimer-fit172-coot.pdb #2/A ARG 444
+PKS13-dimer-fit172-coot.pdb #2/A ARG 504
+PKS13-dimer-fit172-coot.pdb #2/A GLU 549
+PKS13-dimer-fit172-coot.pdb #2/A GLU 602
+PKS13-dimer-fit172-coot.pdb #2/A GLU 609
+PKS13-dimer-fit172-coot.pdb #2/A GLU 619
+PKS13-dimer-fit172-coot.pdb #2/A LYS 687
+PKS13-dimer-fit172-coot.pdb #2/A LYS 696
+PKS13-dimer-fit172-coot.pdb #2/A LYS 743
+PKS13-dimer-fit172-coot.pdb #2/A MET 836
+PKS13-dimer-fit172-coot.pdb #2/A ARG 856
+PKS13-dimer-fit172-coot.pdb #2/A GLU 857
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/A ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/A GLU 1066
+PKS13-dimer-fit172-coot.pdb #2/B GLU 106
+PKS13-dimer-fit172-coot.pdb #2/B GLU 159
+PKS13-dimer-fit172-coot.pdb #2/B GLU 162
+PKS13-dimer-fit172-coot.pdb #2/B GLU 163
+PKS13-dimer-fit172-coot.pdb #2/B ARG 444
+PKS13-dimer-fit172-coot.pdb #2/B ARG 504
+PKS13-dimer-fit172-coot.pdb #2/B GLU 602
+PKS13-dimer-fit172-coot.pdb #2/B GLU 609
+PKS13-dimer-fit172-coot.pdb #2/B GLU 619
+PKS13-dimer-fit172-coot.pdb #2/B LYS 687
+PKS13-dimer-fit172-coot.pdb #2/B LYS 696
+PKS13-dimer-fit172-coot.pdb #2/B LYS 743
+PKS13-dimer-fit172-coot.pdb #2/B MET 836
+PKS13-dimer-fit172-coot.pdb #2/B ARG 856
+PKS13-dimer-fit172-coot.pdb #2/B GLU 857
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/B ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/B GLU 1066
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Hydrogen copy of PKS13-dimer-fit172-coot.pdb #/A PRO 1059 H bonded to atom
+that should not have hydrogens (copy of PKS13-dimer-fit172-coot.pdb #/A PRO
+C)
+> select
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 4 models selected
+> coulombic sel
+The following residues are missing heavy (non-hydrogen) atoms, which may
+result in inaccurate electrostatics:
+PKS13-dimer-fit172-coot.pdb #2/A GLU 106
+PKS13-dimer-fit172-coot.pdb #2/A GLU 159
+PKS13-dimer-fit172-coot.pdb #2/A GLU 162
+PKS13-dimer-fit172-coot.pdb #2/A GLU 163
+PKS13-dimer-fit172-coot.pdb #2/A ARG 444
+PKS13-dimer-fit172-coot.pdb #2/A ARG 504
+PKS13-dimer-fit172-coot.pdb #2/A GLU 549
+PKS13-dimer-fit172-coot.pdb #2/A GLU 602
+PKS13-dimer-fit172-coot.pdb #2/A GLU 609
+PKS13-dimer-fit172-coot.pdb #2/A GLU 619
+PKS13-dimer-fit172-coot.pdb #2/A LYS 687
+PKS13-dimer-fit172-coot.pdb #2/A LYS 696
+PKS13-dimer-fit172-coot.pdb #2/A LYS 743
+PKS13-dimer-fit172-coot.pdb #2/A MET 836
+PKS13-dimer-fit172-coot.pdb #2/A ARG 856
+PKS13-dimer-fit172-coot.pdb #2/A GLU 857
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/A ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/A GLU 1066
+PKS13-dimer-fit172-coot.pdb #2/B GLU 106
+PKS13-dimer-fit172-coot.pdb #2/B GLU 159
+PKS13-dimer-fit172-coot.pdb #2/B GLU 162
+PKS13-dimer-fit172-coot.pdb #2/B GLU 163
+PKS13-dimer-fit172-coot.pdb #2/B ARG 444
+PKS13-dimer-fit172-coot.pdb #2/B ARG 504
+PKS13-dimer-fit172-coot.pdb #2/B GLU 602
+PKS13-dimer-fit172-coot.pdb #2/B GLU 609
+PKS13-dimer-fit172-coot.pdb #2/B GLU 619
+PKS13-dimer-fit172-coot.pdb #2/B LYS 687
+PKS13-dimer-fit172-coot.pdb #2/B LYS 696
+PKS13-dimer-fit172-coot.pdb #2/B LYS 743
+PKS13-dimer-fit172-coot.pdb #2/B MET 836
+PKS13-dimer-fit172-coot.pdb #2/B ARG 856
+PKS13-dimer-fit172-coot.pdb #2/B GLU 857
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/B ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/B GLU 1066
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Hydrogen copy of PKS13-dimer-fit172-coot.pdb #/A PRO 1059 H bonded to atom
+that should not have hydrogens (copy of PKS13-dimer-fit172-coot.pdb #/A PRO
+C)
+> mlp sel
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_A SES surface": minimum
+-27.92, mean -6.306, maximum 23.7
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_B SES surface": minimum
+-28.12, mean -6.405, maximum 22.67
+Map values for surface "PKS13-dimer-fit172-coot.pdb_A SES surface": minimum
+-27.52, mean -4.875, maximum 23.02
+Map values for surface "PKS13-dimer-fit172-coot.pdb_B SES surface": minimum
+-33.11, mean -4.957, maximum 23.04
+To also show corresponding color key, enter the above mlp command and add key
+true
+> coulombic sel
+The following residues are missing heavy (non-hydrogen) atoms, which may
+result in inaccurate electrostatics:
+PKS13-dimer-fit172-coot.pdb #2/A GLU 106
+PKS13-dimer-fit172-coot.pdb #2/A GLU 159
+PKS13-dimer-fit172-coot.pdb #2/A GLU 162
+PKS13-dimer-fit172-coot.pdb #2/A GLU 163
+PKS13-dimer-fit172-coot.pdb #2/A ARG 444
+PKS13-dimer-fit172-coot.pdb #2/A ARG 504
+PKS13-dimer-fit172-coot.pdb #2/A GLU 549
+PKS13-dimer-fit172-coot.pdb #2/A GLU 602
+PKS13-dimer-fit172-coot.pdb #2/A GLU 609
+PKS13-dimer-fit172-coot.pdb #2/A GLU 619
+PKS13-dimer-fit172-coot.pdb #2/A LYS 687
+PKS13-dimer-fit172-coot.pdb #2/A LYS 696
+PKS13-dimer-fit172-coot.pdb #2/A LYS 743
+PKS13-dimer-fit172-coot.pdb #2/A MET 836
+PKS13-dimer-fit172-coot.pdb #2/A ARG 856
+PKS13-dimer-fit172-coot.pdb #2/A GLU 857
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/A ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/A GLU 1066
+PKS13-dimer-fit172-coot.pdb #2/B GLU 106
+PKS13-dimer-fit172-coot.pdb #2/B GLU 159
+PKS13-dimer-fit172-coot.pdb #2/B GLU 162
+PKS13-dimer-fit172-coot.pdb #2/B GLU 163
+PKS13-dimer-fit172-coot.pdb #2/B ARG 444
+PKS13-dimer-fit172-coot.pdb #2/B ARG 504
+PKS13-dimer-fit172-coot.pdb #2/B GLU 602
+PKS13-dimer-fit172-coot.pdb #2/B GLU 609
+PKS13-dimer-fit172-coot.pdb #2/B GLU 619
+PKS13-dimer-fit172-coot.pdb #2/B LYS 687
+PKS13-dimer-fit172-coot.pdb #2/B LYS 696
+PKS13-dimer-fit172-coot.pdb #2/B LYS 743
+PKS13-dimer-fit172-coot.pdb #2/B MET 836
+PKS13-dimer-fit172-coot.pdb #2/B ARG 856
+PKS13-dimer-fit172-coot.pdb #2/B GLU 857
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/B ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/B GLU 1066
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Hydrogen copy of PKS13-dimer-fit172-coot.pdb #/A PRO 1059 H bonded to atom
+that should not have hydrogens (copy of PKS13-dimer-fit172-coot.pdb #/A PRO
+C)
+> transparency (#!1-2 & sel) 40
+> transparency (#!1-2 & sel) 80
+> transparency (#!1-2 & sel) 70
+> select add #2
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 10 models selected
+> select subtract #2
+atoms, 13198 bonds, 4 pseudobonds, 1942 residues, 6 models selected
+> select add #2
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 8 models selected
+> hide #!2 models
+> show #!2 models
+> hide #!1 models
+> show #!1 models
+> preset "molecular surfaces" "atomic coloring (transparent)"
+Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    surface
+    color fromatoms targ s trans 70
+> coulombic sel
+The following residues are missing heavy (non-hydrogen) atoms, which may
+result in inaccurate electrostatics:
+PKS13-dimer-fit172-coot.pdb #2/A GLU 106
+PKS13-dimer-fit172-coot.pdb #2/A GLU 159
+PKS13-dimer-fit172-coot.pdb #2/A GLU 162
+PKS13-dimer-fit172-coot.pdb #2/A GLU 163
+PKS13-dimer-fit172-coot.pdb #2/A ARG 444
+PKS13-dimer-fit172-coot.pdb #2/A ARG 504
+PKS13-dimer-fit172-coot.pdb #2/A GLU 549
+PKS13-dimer-fit172-coot.pdb #2/A GLU 602
+PKS13-dimer-fit172-coot.pdb #2/A GLU 609
+PKS13-dimer-fit172-coot.pdb #2/A GLU 619
+PKS13-dimer-fit172-coot.pdb #2/A LYS 687
+PKS13-dimer-fit172-coot.pdb #2/A LYS 696
+PKS13-dimer-fit172-coot.pdb #2/A LYS 743
+PKS13-dimer-fit172-coot.pdb #2/A MET 836
+PKS13-dimer-fit172-coot.pdb #2/A ARG 856
+PKS13-dimer-fit172-coot.pdb #2/A GLU 857
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/A ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/A LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/A GLU 1066
+PKS13-dimer-fit172-coot.pdb #2/B GLU 106
+PKS13-dimer-fit172-coot.pdb #2/B GLU 159
+PKS13-dimer-fit172-coot.pdb #2/B GLU 162
+PKS13-dimer-fit172-coot.pdb #2/B GLU 163
+PKS13-dimer-fit172-coot.pdb #2/B ARG 444
+PKS13-dimer-fit172-coot.pdb #2/B ARG 504
+PKS13-dimer-fit172-coot.pdb #2/B GLU 602
+PKS13-dimer-fit172-coot.pdb #2/B GLU 609
+PKS13-dimer-fit172-coot.pdb #2/B GLU 619
+PKS13-dimer-fit172-coot.pdb #2/B LYS 687
+PKS13-dimer-fit172-coot.pdb #2/B LYS 696
+PKS13-dimer-fit172-coot.pdb #2/B LYS 743
+PKS13-dimer-fit172-coot.pdb #2/B MET 836
+PKS13-dimer-fit172-coot.pdb #2/B ARG 856
+PKS13-dimer-fit172-coot.pdb #2/B GLU 857
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1018
+PKS13-dimer-fit172-coot.pdb #2/B ARG 1047
+PKS13-dimer-fit172-coot.pdb #2/B LYS 1065
+PKS13-dimer-fit172-coot.pdb #2/B GLU 1066
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Hydrogen copy of PKS13-dimer-fit172-coot.pdb #/A PRO 1059 H bonded to atom
+that should not have hydrogens (copy of PKS13-dimer-fit172-coot.pdb #/A PRO
+C)
+> transparency (#!1-2 & sel) 80
+> preset "molecular surfaces" "ghostly white"
+Using preset: Molecular Surfaces / Ghostly White
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    surface
+    color white targ s trans 80
+> select clear
+> preset "overall look" "publication 2 (depth-cued)"
+Using preset: Overall Look / Publication 2 (Depth-Cued)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes f
+    lighting depthCue t
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+> select clear
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting flat
+> lighting full
+> lighting soft
+> lighting simple
+> graphics silhouettes false
+> graphics silhouettes true
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+Drag select of 2qo3 KS3AT3 cerulenin.pdb_B SES surface, 11510 of 662528
+triangles, PKS13-dimer-fit172-coot.pdb_A SES surface, 8896 of 715666
+triangles, 37 residues
+Drag select of 2qo3 KS3AT3 cerulenin.pdb_A SES surface, 14660 of 663312
+triangles, 2qo3 KS3AT3 cerulenin.pdb_B SES surface, 61434 of 662528 triangles,
+cap near, 95 of 1545 triangles, PKS13-dimer-fit172-coot.pdb_A SES surface,
+of 715666 triangles, PKS13-dimer-fit172-coot.pdb_B SES surface, 12119 of
+triangles, 266 residues, 1 pseudobonds
+> ui mousemode right translate
+> select #1/A
+atoms, 6584 bonds, 2 pseudobonds, 967 residues, 2 models selected
+> ui mousemode right select
+Drag select of 2qo3 KS3AT3 cerulenin.pdb_A SES surface, 316335 of 663312
+triangles, 2qo3 KS3AT3 cerulenin.pdb_B SES surface, 290909 of 662528
+triangles, PKS13-dimer-fit172-coot.pdb_A SES surface, 322303 of 715666
+triangles, PKS13-dimer-fit172-coot.pdb_B SES surface, 343513 of 707554
+triangles, 16 atoms, 1751 residues, 4 pseudobonds, 14 bonds
+> ui tool show Matchmaker
+> matchmaker #!2 & sel to #1 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1083.5
+RMSD between 376 pruned atom pairs is 0.917 angstroms; (across all 434 pairs:
+.054)
+> matchmaker #!2 & sel to #1 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1083.5
+RMSD between 376 pruned atom pairs is 0.917 angstroms; (across all 434 pairs:
+.054)
+> matchmaker #!2 & sel to #1 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1083.5
+RMSD between 376 pruned atom pairs is 0.917 angstroms; (across all 434 pairs:
+.054)
+> select clear
+> ui mousemode right translate
+> ui mousemode right zoom
+> ui mousemode right select
+> select #1/B:202@SG
+atom, 1 residue, 1 model selected
+> show sel atoms
+> select #2/A:286@CA
+atom, 1 residue, 1 model selected
+> select #1/B:202@N
+atom, 1 residue, 1 model selected
+> show sel atoms
+Drag select of 2qo3 KS3AT3 cerulenin.pdb_A SES surface, 1428 of 663312
+triangles, 2qo3 KS3AT3 cerulenin.pdb_B SES surface, 2767 of 662528 triangles,
+cap near, 95 of 13702 triangles, PKS13-dimer-fit172-coot.pdb_A SES surface,
+of 715666 triangles, cap near, 92 of 11934 triangles, PKS13-dimer-
+fit172-coot.pdb_B SES surface, 4026 of 707554 triangles, 1 atoms, 18 residues,
+bonds
+> select #1.3.1
+model selected
+> select #2.2.1
+model selected
+> ui mousemode right select
+> select #2.2.1
+model selected
+> select #2.2.1
+model selected
+> select #1.3.1
+model selected
+> select #1.3.1
+model selected
+> ui mousemode right translate
+> ui mousemode right zoom
+> ui mousemode right translate
+> ui mousemode right select
+> select clear
+> select #1.3.1
+model selected
+> select #1.3.1
+model selected
+> select #1/B:202@CB
+atom, 1 residue, 1 model selected
+> show sel atoms
+> select #1/B:202@SG
+atom, 1 residue, 1 model selected
+> select #1/B:202@CB
+atom, 1 residue, 1 model selected
+> hide #!1 models
+> select #2/A:287@N
+atom, 1 residue, 1 model selected
+> show sel atoms
+> style sel stick
+Changed 1 atom style
+> hide sel cartoons
+> show sel atoms
+Drag select of PKS13-dimer-fit172-coot.pdb_A SES surface, 307 of 715666
+triangles, PKS13-dimer-fit172-coot.pdb_B SES surface, 67 of 707554 triangles,
+cap near, 18 of 24878 triangles, 1 residues
+> show #!1 models
+> select #1.2.2
+model selected
+> show atoms
+> undo
+> ui mousemode right select
+> select #1.2.2
+model selected
+> select #1.2.2
+model selected
+> select #1.2.2
+model selected
+> select add #1
+atoms, 13198 bonds, 4 pseudobonds, 1942 residues, 6 models selected
+> select subtract #1
+models selected
+> hide #!1 models
+> select #2.3.1
+model selected
+Drag select of PKS13-dimer-fit172-coot.pdb_A SES surface, 26 of 715666
+triangles, PKS13-dimer-fit172-coot.pdb_B SES surface, 13 of 707554 triangles,
+residues
+> select
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 8 models selected
+> hide sel & #!2 surfaces
+> show #!1 models
+> select #1.2.1
+model selected
+> hide surfaces
+> select #2/B:287
+atoms, 5 bonds, 1 residue, 1 model selected
+> nucleotides sel atoms
+> style nucleic & sel stick
+Changed 0 atom styles
+> show sel atoms
+> select #1/A:202
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> mlp sel
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_A SES surface": minimum
+-27.92, mean -6.306, maximum 23.7
+To also show corresponding color key, enter the above mlp command and add key
+true
+> select
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 12 models selected
+> mlp sel
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_A SES surface": minimum
+-27.92, mean -6.306, maximum 23.7
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_B SES surface": minimum
+-28.12, mean -6.405, maximum 22.67
+Map values for surface "PKS13-dimer-fit172-coot.pdb_A SES surface": minimum
+-27.58, mean -4.875, maximum 23.02
+Map values for surface "PKS13-dimer-fit172-coot.pdb_B SES surface": minimum
+-32.81, mean -4.957, maximum 22.96
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide sel surfaces
+> select clear
+> select #1/B:202
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide #!1 models
+> select #2/A:235
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #2/A:290
+atoms, 5 bonds, 1 residue, 1 model selected
+> select #2/A:235
+atoms, 7 bonds, 1 residue, 1 model selected
+> select
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 8 models selected
+> show sel & #!2 cartoons
+> select #2/A:287
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> show #!1 models
+> select add #1
+atoms, 13203 bonds, 4 pseudobonds, 1943 residues, 4 models selected
+> select add #2
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 11 models selected
+> select subtract #2
+atoms, 13198 bonds, 4 pseudobonds, 1942 residues, 6 models selected
+> select subtract #1
+models selected
+> ui mousemode right zoom
+> lighting full
+> lighting soft
+> lighting simple
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting flat
+> lighting full
+> lighting soft
+> lighting simple
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+> preset "overall look" "publication 2 (depth-cued)"
+Using preset: Overall Look / Publication 2 (Depth-Cued)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes f
+    lighting depthCue t
+> lighting simple
+> lighting full
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting flat
+> lighting simple
+> lighting flat
+> lighting full
+> lighting simple
+> lighting soft
+> graphics silhouettes false
+> lighting simple
+> hide #!1 models
+> show #!1 models
+> ui tool show Matchmaker
+> matchmaker #!2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1858.5
+RMSD between 320 pruned atom pairs is 0.886 angstroms; (across all 857 pairs:
+.486)
+> matchmaker #!2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1858.5
+RMSD between 320 pruned atom pairs is 0.886 angstroms; (across all 857 pairs:
+.486)
+> matchmaker #!2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 1858.5
+RMSD between 320 pruned atom pairs is 0.886 angstroms; (across all 857 pairs:
+.486)
+> help help:credits.html
+> preset "molecular surfaces" "ghostly white"
+Using preset: Molecular Surfaces / Ghostly White
+Changed 0 atom styles
+Preset expands to these ChimeraX commands:
+    style (protein|nucleic|solvent) & @@draw_mode=0 stick
+    surface
+    color white targ s trans 80
+> transparency 80
+> select #1/A#1/B
+atoms, 13198 bonds, 4 pseudobonds, 1942 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel wheat target s
+> color sel tan target s
+> color sel pale goldenrod target s
+> color sel goldenrod target s
+> color sel wheat target s
+> transparency (#!1 & sel) 20
+> transparency (#!1 & sel) 90
+> transparency (#!1 & sel) 80
+> select #2/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> select add #2.3
+atoms, 7047 bonds, 1 pseudobond, 1845 residues, 5 models selected
+> select add #2.2
+atoms, 7047 bonds, 1 pseudobond, 1845 residues, 8 models selected
+> select add #2.1
+atoms, 7047 bonds, 2 pseudobonds, 1845 residues, 8 models selected
+> select subtract #2.1
+atoms, 7047 bonds, 1845 residues, 7 models selected
+> select add #2
+atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 8 models selected
+> select subtract #2
+models selected
+> ui tool show "Color Actions"
+> color light sky blue target s
+> color powder blue target s
+> undo
+> color #2.2 #c4ffffff
+> color #2.3 #c5ffffff
+> select add #2.2
+atoms, 922 residues, 3 models selected
+> select add #2.3
+atoms, 1845 residues, 6 models selected
+> transparency (#!2 & sel) 80
+> select clear
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image2.png supersample 3
+> save /Users/sarah/Desktop/image3.png supersample 3
+> select
+atoms, 27297 bonds, 6 pseudobonds, 3787 residues, 12 models selected
+> hide sel surfaces
+> select clear
+> ui mousemode right select
+> select ::name="CER"
+atoms, 14 bonds, 2 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum target s
+> ui tool show "Color Actions"
+> color sel plum target ac
+> color sel byhetero target ac
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/A #1/B
+Alignment identifier is 1
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/A #1/B
+Alignment identifier is 2
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/A #1/B
+Alignment identifier is 3
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/A #1/B
+Alignment identifier is 4
+> select
+> #1/A-B:33-41,64-65,92-93,101-102,148-152,195-199,224-230,268-276,289-298,333-335,366-369,398-399,419-421,426-427,436-442,447-455,472-478,518-524,547-551,559-563,646-649,688-692,714-717,720-725,744-746,780-782,789-790,808-809,824-827,852-854,903-904
+atoms, 2012 bonds, 286 residues, 1 model selected
+> select
+> #1/A-B:42-46,48-58,73-78,103-108,110-135,138-143,170-175,177-190,200-218,235-244,277-284,309-325,327-331,343-355,370-376,378-397,480-496,501-512,526-540,574-599,602-609,618-640,652-662,665-683,695-707,726-742,755-770,791-806,809-820,834-844,862-877,882-887
+atoms, 6332 bonds, 834 residues, 1 model selected
+> select #1/A-B:377
+atoms, 20 bonds, 2 residues, 1 model selected
+> select #1/A-B:377
+atoms, 20 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #1/A-B:337
+atoms, 20 bonds, 2 residues, 1 model selected
+> select #1/A-B:337
+atoms, 20 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #1/A-B:442
+atoms, 22 bonds, 2 residues, 1 model selected
+> select #1/A-B:442
+atoms, 22 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select #2/B:463
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:423
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:423@NE2
+atom, 1 residue, 1 model selected
+> select #1/A:960@O2
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> select clear
+> distance #1/A:960@O2 #2/B:423@NE2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 O2 and PKS13-dimer-
+fit172-coot.pdb #2/B HIS 423 NE2: 3.089Å
+> distance #2/B:463@NE2 #1/A:960@O2
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2 and 2qo3 KS3AT3
+cerulenin.pdb #1/A CER 960 O2: 2.657Å
+> ui mousemode right select
+> select clear
+> select #2/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> ui mousemode right distance
+> select clear
+> distance #1/A:960@N1 #2/B:528@O
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 N1 and PKS13-dimer-
+fit172-coot.pdb #2/B PHE 528 O: 3.674Å
+> ui mousemode right select
+> select #2/B:528@C
+atom, 1 residue, 1 model selected
+> show sel cartoons
+> color #3 #44fa9fff models
+> ui mousemode right distance
+> hide #!2 models
+> distance #1/A:337@NE2 #1/A:960@O2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A HIS 337 NE2 and CER 960 O2:
+.382Å
+> distance #1/A:377@NE2 #1/A:960@O2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A HIS 377 NE2 and CER 960 O2:
+.748Å
+> ui mousemode right select
+> select clear
+> select #1/A:442
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select clear
+> ui mousemode right distance
+> distance #1/A:442@C #1/A:960@N1
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A PHE 442 C and CER 960 N1:
+.373Å
+> show #!2 models
+> ui mousemode right select
+> show sel cartoons
+> hide #3.1 models
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image2.png supersample 3
+> lighting full
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting shadows false
+> lighting shadows true
+> lighting full
+> save /Users/sarah/Desktop/image3.png supersample 3
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting shadows true
+> lighting flat
+> preset "overall look" "publication 2 (depth-cued)"
+Using preset: Overall Look / Publication 2 (Depth-Cued)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes f
+    lighting depthCue t
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+> lighting simple
+> save /Users/sarah/Desktop/image4.png supersample 3
+> select
+atoms, 27297 bonds, 12 pseudobonds, 3787 residues, 10 models selected
+> mlp sel
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_A SES surface": minimum
+-27.92, mean -6.306, maximum 23.7
+Map values for surface "2qo3 KS3AT3 cerulenin.pdb_B SES surface": minimum
+-28.12, mean -6.405, maximum 22.67
+Map values for surface "PKS13-dimer-fit172-coot.pdb_A SES surface": minimum
+-27.52, mean -4.875, maximum 23.02
+Map values for surface "PKS13-dimer-fit172-coot.pdb_B SES surface": minimum
+-33.11, mean -4.957, maximum 23.04
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide #!2.2 models
+> hide #!2.3 models
+> select
+atoms, 27297 bonds, 12 pseudobonds, 3787 residues, 10 models selected
+> hide sel surfaces
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> show sel surfaces
+> hide sel surfaces
+> select clear
+> ui mousemode right translate
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> show sel surfaces
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.77801,-0.4344,-0.45388,30.808,-0.49443,-0.86907,-0.015756,288.44,-0.38761,0.23667,-0.89092,226.4
+> hide sel surfaces
+> view matrix models
+> #2,0.77801,-0.4344,-0.45388,30.715,-0.49443,-0.86907,-0.015756,289.23,-0.38761,0.23667,-0.89092,227.18
+> view matrix models
+> #2,0.77801,-0.4344,-0.45388,30.623,-0.49443,-0.86907,-0.015756,288.89,-0.38761,0.23667,-0.89092,227.39
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.78482,-0.43491,-0.44148,26.859,-0.49112,-0.87096,-0.015046,288.47,-0.37797,0.22863,-0.89714,228.38
+> view matrix models
+> #2,0.78074,-0.44609,-0.43756,29.272,-0.50394,-0.86354,-0.01881,290.26,-0.36945,0.23519,-0.89899,225.63
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.78074,-0.44609,-0.43756,29.422,-0.50394,-0.86354,-0.01881,290.14,-0.36945,0.23519,-0.89899,225.55
+> view matrix models
+> #2,0.78074,-0.44609,-0.43756,29.455,-0.50394,-0.86354,-0.01881,290.24,-0.36945,0.23519,-0.89899,225.48
+> view matrix models
+> #2,0.78074,-0.44609,-0.43756,29.444,-0.50394,-0.86354,-0.01881,290.2,-0.36945,0.23519,-0.89899,225.51
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.7672,-0.47962,-0.42587,36.965,-0.54201,-0.83982,-0.030616,295.29,-0.34297,0.25431,-0.90427,217.11
+> view matrix models
+> #2,0.75502,-0.47662,-0.45031,43.714,-0.54879,-0.83518,-0.036145,296.8,-0.35886,0.27441,-0.89214,213.66
+> view matrix models
+> #2,0.74956,-0.49017,-0.44484,46.601,-0.55656,-0.8305,-0.022675,294.69,-0.35833,0.26458,-0.89532,216.27
+> ui mousemode right select
+Drag select of 58 atoms, 189 residues, 56 bonds, 6 pseudobonds
+Drag select of 54 atoms, 130 residues, 52 bonds, 6 pseudobonds
+> ui tool show Matchmaker
+> matchmaker #!2 & sel to #1 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 185.6
+RMSD between 52 pruned atom pairs is 0.670 angstroms; (across all 53 pairs:
+.774)
+> matchmaker #!2 & sel to #1 & sel
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 2qo3 KS3AT3 cerulenin.pdb, chain A (#1) with PKS13-dimer-
+fit172-coot.pdb, chain B (#2), sequence alignment score = 185.6
+RMSD between 52 pruned atom pairs is 0.670 angstroms; (across all 53 pairs:
+.774)
+> select #2/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> mlp sel
+Map values for surface "PKS13-dimer-fit172-coot.pdb_B SES surface": minimum
+-33.58, mean -4.956, maximum 22.55
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide sel surfaces
+Drag select of 5 residues
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.7767,-0.4319,-0.45849,30.996,-0.50644,-0.861,-0.046874,294.97,-0.37451,0.2686,-0.88746,217.26
+> view matrix models
+> #2,0.7767,-0.4319,-0.45849,31.095,-0.50644,-0.861,-0.046874,295.22,-0.37451,0.2686,-0.88746,217.21
+> view matrix models
+> #2,0.7767,-0.4319,-0.45849,32.072,-0.50644,-0.861,-0.046874,296.15,-0.37451,0.2686,-0.88746,218.21
+> undo
+> view matrix models
+> #2,0.7767,-0.4319,-0.45849,30.59,-0.50644,-0.861,-0.046874,294.71,-0.37451,0.2686,-0.88746,216.65
+> undo
+> view matrix models
+> #2,0.7767,-0.4319,-0.45849,31.063,-0.50644,-0.861,-0.046874,295.21,-0.37451,0.2686,-0.88746,217.2
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.78254,-0.44423,-0.43623,28.026,-0.50867,-0.86019,-0.036527,293.42,-0.35902,0.25048,-0.89909,220.22
+> ui mousemode right "translate selected models"
+> view matrix models
+> #2,0.78254,-0.44423,-0.43623,28.348,-0.50867,-0.86019,-0.036527,293.48,-0.35902,0.25048,-0.89909,220.37
+> view matrix models
+> #2,0.78254,-0.44423,-0.43623,28.449,-0.50867,-0.86019,-0.036527,293.57,-0.35902,0.25048,-0.89909,220.15
+> view matrix models
+> #2,0.78254,-0.44423,-0.43623,28.368,-0.50867,-0.86019,-0.036527,293.59,-0.35902,0.25048,-0.89909,220.04
+> mlp sel
+Map values for surface "PKS13-dimer-fit172-coot.pdb_B SES surface": minimum
+-32.98, mean -4.956, maximum 22.9
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide sel surfaces
+> mlp sel
+Map values for surface "PKS13-dimer-fit172-coot.pdb_B SES surface": minimum
+-32.98, mean -4.956, maximum 22.9
+To also show corresponding color key, enter the above mlp command and add key
+true
+> hide sel surfaces
+> ui mousemode right "rotate selected models"
+> view matrix models
+> #2,0.79423,-0.43054,-0.42876,21.584,-0.49678,-0.86642,-0.050211,295.23,-0.34987,0.25288,-0.90202,218.26
+> view matrix models
+> #2,0.78868,-0.43252,-0.43693,24.775,-0.49731,-0.86666,-0.039745,293.29,-0.36148,0.24864,-0.89862,220.84
+> show sel surfaces
+> ui tool show "Color Actions"
+> color sel light blue target s
+> show sel surfaces
+> select #2/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> show sel surfaces
+> ui tool show "Color Actions"
+> color sel light blue target s
+> select clear
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image5.png supersample 3
+> preset "overall look" "publication 2 (depth-cued)"
+Using preset: Overall Look / Publication 2 (Depth-Cued)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes f
+    lighting depthCue t
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+> preset "overall look" interactive
+Using preset: Overall Look / Interactive
+> set bgColor transparent
+Preset expands to these ChimeraX commands:
+    ~set bg
+    graphics silhouettes f
+    lighting depthCue t
+> save /Users/sarah/Desktop/image6.png supersample 3
+> hide atoms
+> undo
+> select
+atoms, 27297 bonds, 12 pseudobonds, 3787 residues, 14 models selected
+> hide sel surfaces
+> set bgColor white
+> set bgColor #ffffff00
+> open "/Users/sarah/Documents/Work/PKS13/2gfx FabF platensimycin.pdb"
+gfx FabF platensimycin.pdb title:
+Structure of E. Coli fabf(C163Q) In complex with platensimycin [more info...]
+Chain information for 2gfx FabF platensimycin.pdb #4
+---
+Chain | Description | UniProt
+A | 3-oxoacyl-[ACYL-carrier-protein] synthase II; β-ketoacyl- ACP synthase II;
+KAS II; FABF | FABF_ECOLI 1-412
+Non-standard residues in 2gfx FabF platensimycin.pdb #4
+---
+PMN — platensimycin
+> color #4 #d1b58cff
+> select add #4
+atoms, 30393 bonds, 12 pseudobonds, 4309 residues, 19 models selected
+> ui tool show "Color Actions"
+> color sel byhetero target s
+> hide #!1 models
+> select subtract #1
+atoms, 17195 bonds, 2 pseudobonds, 2367 residues, 12 models selected
+> ui tool show Matchmaker
+> matchmaker #4 to #2
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#2) with 2gfx FabF
+platensimycin.pdb, chain A (#4), sequence alignment score = 656.7
+RMSD between 261 pruned atom pairs is 1.122 angstroms; (across all 400 pairs:
+.638)
+> matchmaker #4 to #2
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#2) with 2gfx FabF
+platensimycin.pdb, chain A (#4), sequence alignment score = 656.7
+RMSD between 261 pruned atom pairs is 1.122 angstroms; (across all 400 pairs:
+.638)
+> select #2/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> show sel surfaces
+> hide #!2.3 models
+> show #2.3 models
+> hide #!2.2 models
+> show #2.2 models
+> ui tool show "Color Actions"
+> color sel light blue target s
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel light blue target s
+> show sel surfaces
+> select add #4
+atoms, 10148 bonds, 1 pseudobond, 1445 residues, 4 models selected
+> show sel surfaces
+> select
+atoms, 30393 bonds, 12 pseudobonds, 4309 residues, 9 models selected
+> transparency (#!2,4 & sel) 80
+> select clear
+> select #4/A
+atoms, 3096 bonds, 522 residues, 1 model selected
+> hide sel atoms
+> select clear
+> save /Users/sarah/Desktop/image7.png supersample 3
+> save /Users/sarah/Desktop/image8.png supersample 3
+> select ::name="PMN"
+atoms, 36 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel plum target s
+> color sel byhetero target a
+> show sel atoms
+> ui tool show "Color Actions"
+> color sel plum target ac
+> color sel byhetero target ac
+> ui mousemode right translate
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/A
+Alignment identifier is 4/A
+> select #4/A:163
+atoms, 8 bonds, 1 residue, 1 model selected
+> select #4/A:163
+atoms, 8 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4/A:340
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #4/A:340
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4/A:303
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #4/A:303
+atoms, 10 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #4/A:309
+atoms, 4 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> select add #4
+atoms, 3096 bonds, 522 residues, 3 models selected
+> color (#!4 & sel) byhetero
+> hide sel surfaces
+> hide #!2.2 models
+> hide #!2.3 models
+> select #4/A:400
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #4/A:400
+atoms, 11 bonds, 1 residue, 1 model selected
+> show sel atoms
+> ui mousemode right select
+> select #2/B:530
+atoms, 11 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4/A:392
+atoms, 12 bonds, 1 residue, 1 model selected
+> select #4/A:392
+atoms, 12 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> ui mousemode right translate
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> ui mousemode right select
+> select #2/B:392
+atoms, 7 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:463@NE2
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> distance #2/B:463@NE2 #4/A:1001@O33
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2 and 2gfx FabF
+platensimycin.pdb #4/A PMN 1001 O33: 3.288Å
+> ~distance #2/B:463@NE2 #4/A:1001@O33
+> distance #4/A:1001@O33 #2/B:463@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and
+PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2: 3.288Å
+> distance #2/B:463@NE2 #2/B:423@NE2
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2 and HIS 423 NE2:
+.792Å
+> ~distance #2/B:463@NE2 #2/B:423@NE2
+> ~distance #2/B:463@NE2 #1/A:960@O2
+> ~distance #1/A:377@NE2 #1/A:960@O2
+> ~distance #1/A:960@O2 #2/B:423@NE2
+> distance #2/B:423@NE2 #4/A:1001@O33
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 423 NE2 and 2gfx FabF
+platensimycin.pdb #4/A PMN 1001 O33: 2.290Å
+> distance #4/A:1001@O33 #4/A:309@N
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and ALA 309 N:
+.371Å
+> ~distance #4/A:1001@O33 #4/A:309@N
+> distance #4/A:309@N #4/A:1001@O19
+Distance between 2gfx FabF platensimycin.pdb #4/A ALA 309 N and PMN 1001 O19:
+.034Å
+> ui mousemode right select
+> select #4/A:309@CA
+atom, 1 residue, 1 model selected
+> show sel cartoons
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #2/B:392
+atoms, 7 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> ui mousemode right distance
+> distance #4/A:1001@O19 #2/B:392@O
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O19 and
+PKS13-dimer-fit172-coot.pdb #2/B ILE 392 O: 6.830Å
+> distance #2/B:392@O #4/A:1001@N28
+Distance between PKS13-dimer-fit172-coot.pdb #2/B ILE 392 O and 2gfx FabF
+platensimycin.pdb #4/A PMN 1001 N28: 3.314Å
+> distance #4/A:1001@N28 #4/A:270@O
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 N28 and THR 270 O:
+.908Å
+> ~distance #4/A:309@N #4/A:1001@O19
+> ~distance #4/A:1001@O19 #2/B:392@O
+> distance #4/A:270@O #4/A:1001@O19
+Distance between 2gfx FabF platensimycin.pdb #4/A THR 270 O and PMN 1001 O19:
+.681Å
+> ~distance #4/A:270@O #4/A:1001@O19
+> ui mousemode right select
+> show sel cartoons
+> color #3 #5afac6ff models
+> color #3 #51fad4ff models
+> ui mousemode right select
+> color #3 #a9ab00ff models
+> color #3 #fdff00ff models
+> ui mousemode right distance
+> ~distance #1/A:337@NE2 #1/A:960@O2
+> distance #4/A:1001@O19 #4/A:1001@O33
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O19 and O33:
+.518Å
+> distance #4/A:1001@O33 #4/A:340@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and HIS 340
+NE2: 2.829Å
+> ~distance #4/A:1001@O19 #4/A:1001@O33
+> color #3 #46fd8dff models
+> color #3 #44fda4ff models
+> color #3 #3bfda5ff models
+> ui mousemode right distance
+> ~distance #4/A:1001@O33 #4/A:340@NE2
+> distance #4/A:340@NE2 #2/B:287@CB
+Distance between 2gfx FabF platensimycin.pdb #4/A HIS 340 NE2 and PKS13-dimer-
+fit172-coot.pdb #2/B CYS 287 CB: 3.908Å
+> distance #2/B:287@CB #4/A:340@NE2
+Distance already exists; modify distance properties with 'distance style'
+> ~distance #4/A:340@NE2 #2/B:287@CB
+> distance #4/A:340@NE2 #4/A:163@CB
+Distance between 2gfx FabF platensimycin.pdb #4/A HIS 340 NE2 and GLN 163 CB:
+.810Å
+> ~distance #4/A:340@NE2 #4/A:163@CB
+> distance #4/A:1001@O33 #4/A:340@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and HIS 340
+NE2: 2.829Å
+> ~distance #4/A:1001@O33 #4/A:340@NE2
+> distance #4/A:340@NE2 #4/A:1001@O33
+Distance between 2gfx FabF platensimycin.pdb #4/A HIS 340 NE2 and PMN 1001
+O33: 2.829Å
+> distance #4/A:1001@O33 #4/A:303@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O33 and HIS 303
+NE2: 2.586Å
+> ui mousemode right select
+> hide sel cartoons
+> ui mousemode right distance
+> distance #4/A:303@NE2 #4/A:309@N
+Distance between 2gfx FabF platensimycin.pdb #4/A HIS 303 NE2 and ALA 309 N:
+.794Å
+> distance #4/A:309@N #4/A:1001@O19
+Distance between 2gfx FabF platensimycin.pdb #4/A ALA 309 N and PMN 1001 O19:
+.034Å
+> ~distance #4/A:303@NE2 #4/A:309@N
+> show sel cartoons
+> ui mousemode right select
+> select #4/A:270
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> ui mousemode right distance
+> ~distance #4/A:1001@N28 #4/A:270@O
+> distance #4/A:1001@O19 #4/A:1001@N28
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 O19 and N28: 5.714Å
+> ~distance #4/A:1001@O19 #4/A:1001@N28
+> distance #4/A:1001@N28 #4/A:270@O
+Distance between 2gfx FabF platensimycin.pdb #4/A PMN 1001 N28 and THR 270 O:
+.908Å
+> ui mousemode right select
+> show sel cartoons
+> ui mousemode right translate
+> ui mousemode right select
+> select #4/A:207
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select #2/B:348
+atoms, 3 bonds, 1 residue, 1 model selected
+> hide sel bonds
+> select add #2/B:349
+atoms, 15 bonds, 2 residues, 2 models selected
+> select add #4/A:228
+atoms, 18 bonds, 3 residues, 3 models selected
+> select add #4/A:229
+atoms, 29 bonds, 4 residues, 4 models selected
+> select add #2/B:350
+atoms, 35 bonds, 5 residues, 4 models selected
+> select add #4/A:230
+atoms, 41 bonds, 6 residues, 4 models selected
+> select add #4/A:231
+atoms, 48 bonds, 7 residues, 4 models selected
+> select add #2/B:351
+atoms, 58 bonds, 8 residues, 4 models selected
+> select add #4/A:232
+atoms, 61 bonds, 9 residues, 4 models selected
+> select add #2/B:352
+atoms, 66 bonds, 10 residues, 4 models selected
+> hide sel cartoons
+> select #4/A:227
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #2/B:347
+atoms, 14 bonds, 2 residues, 3 models selected
+> hide sel cartoons
+> select #4/A:218
+atoms, 4 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #4/A:219
+atoms, 5 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> ui mousemode right translate
+> ui mousemode right select
+Drag select of 1 residues
+> select #4/A:208
+atoms, 7 bonds, 1 residue, 1 model selected
+> select add #2/B:332
+atoms, 13 bonds, 2 residues, 3 models selected
+> hide sel cartoons
+> select #2/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> undo
+> select clear
+Drag select of 3 residues
+> select clear
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image9.png supersample 3
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+> save /Users/sarah/Desktop/image10.png supersample 3
+> lighting simple
+> save /Users/sarah/Desktop/image11.png supersample 3
+> lighting full
+> lighting simple
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes false
+> lighting full
+> lighting soft
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting flat
+> lighting full
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting soft
+> graphics silhouettes true
+> lighting full
+> graphics silhouettes false
+> lighting simple
+> lighting soft
+> lighting simple
+> lighting full
+> save /Users/sarah/Desktop/image12.png supersample 3
+> select
+atoms, 30393 bonds, 15 pseudobonds, 4309 residues, 8 models selected
+> show sel & #!2,4 cartoons
+> select clear
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> show sel surfaces
+> surface style #!2.3 solid
+> transparency (#!2 & sel) 0
+> select clear
+> select #2/A
+atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
+> show sel surfaces
+> transparency (#!2 & sel) 0
+> select clear
+> save /Users/sarah/Desktop/image13.png supersample 3
+> lighting full
+> graphics silhouettes true
+> save /Users/sarah/Desktop/image14.png supersample 3
+> select
+atoms, 30393 bonds, 15 pseudobonds, 4309 residues, 12 models selected
+> hide sel & #!2,4 surfaces
+> select clear
+> ui mousemode right select
+> select #2/B:332
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select add #4/A:208
+atoms, 13 bonds, 2 residues, 3 models selected
+> select add #4/A:207
+atoms, 17 bonds, 3 residues, 4 models selected
+> hide sel cartoons
+> select clear
+> select #2/B:351
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #2/B:350
+atoms, 16 bonds, 2 residues, 2 models selected
+> select subtract #2/B:350
+atoms, 10 bonds, 1 residue, 2 models selected
+> select add #2/B:350
+atoms, 16 bonds, 2 residues, 2 models selected
+> select add #4/A:231
+atoms, 23 bonds, 3 residues, 3 models selected
+> select add #4/A:230
+atoms, 29 bonds, 4 residues, 4 models selected
+> select add #4/A:229
+atoms, 40 bonds, 5 residues, 4 models selected
+> select add #4/A:228
+atoms, 43 bonds, 6 residues, 4 models selected
+> select add #4/A:227
+atoms, 50 bonds, 7 residues, 4 models selected
+> select add #2/B:347
+atoms, 57 bonds, 8 residues, 4 models selected
+> select add #4/A:226
+atoms, 67 bonds, 9 residues, 4 models selected
+> select add #2/B:348
+atoms, 70 bonds, 10 residues, 4 models selected
+> select add #4/A:225
+atoms, 78 bonds, 11 residues, 4 models selected
+> select add #2/B:349
+atoms, 90 bonds, 12 residues, 4 models selected
+> select subtract #2/B:349
+atoms, 78 bonds, 11 residues, 4 models selected
+> hide sel cartoons
+> select add #2/B:349
+atoms, 90 bonds, 12 residues, 4 models selected
+> select add #2/B:352
+atoms, 95 bonds, 13 residues, 4 models selected
+> select add #4/A:232
+atoms, 98 bonds, 14 residues, 4 models selected
+> hide sel cartoons
+> save /Users/sarah/Desktop/image15.png supersample 3
+> graphics silhouettes false
+> save /Users/sarah/Desktop/image16.png supersample 3
+> lighting full
+> lighting simple
+> save /Users/sarah/Desktop/image17.png supersample 3
+> hide #!4 models
+> show #!1 models
+> select #2/B:530
+atoms, 11 bonds, 1 residue, 1 model selected
+> undo
+> show #!1 models
+> ui mousemode right select
+> select #2/B:530
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel bonds
+> hide sel atoms
+> select #2/B:392@CB
+atom, 1 residue, 1 model selected
+> select #2/B:392@CB
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> show sel cartoons
+> select #2/B:392@CD1
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/B:392@CG1
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/B:392@CG2
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/B:346
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #1/A:266
+atoms, 9 bonds, 2 residues, 3 models selected
+> select add #1/A:265
+atoms, 20 bonds, 3 residues, 4 models selected
+> select add #1/A:264
+atoms, 23 bonds, 4 residues, 4 models selected
+> select add #1/A:263
+atoms, 34 bonds, 5 residues, 4 models selected
+> select add #1/A:262
+atoms, 37 bonds, 6 residues, 4 models selected
+> select add #1/A:261
+atoms, 44 bonds, 7 residues, 4 models selected
+> hide sel cartoons
+> select add #1/A:260
+atoms, 48 bonds, 8 residues, 4 models selected
+> hide sel cartoons
+> ui mousemode right distance
+> distance #4/A:270@O #2/B:423@NE2
+Distance between 2gfx FabF platensimycin.pdb #4/A THR 270 O and PKS13-dimer-
+fit172-coot.pdb #2/B HIS 423 NE2: 9.269Å
+> distance #2/B:423@NE2 #1/A:960@O2
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 423 NE2 and 2qo3 KS3AT3
+cerulenin.pdb #1/A CER 960 O2: 3.563Å
+> distance #2/B:463@NE2 #1/A:960@O2
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2 and 2qo3 KS3AT3
+cerulenin.pdb #1/A CER 960 O2: 2.861Å
+> ~distance #2/B:463@NE2 #1/A:960@O2
+> ui mousemode right select
+> select #2/B:528
+atoms, 11 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> ui mousemode right distance
+> ~distance #1/A:960@N1 #2/B:528@O
+> distance #1/A:960@N1 #2/B:528@O
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 N1 and PKS13-dimer-
+fit172-coot.pdb #2/B PHE 528 O: 4.270Å
+> show sel cartoons
+> show sel atoms
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> color #3 #f8dc47ff models
+> color #3 #66f69eff models
+> ui mousemode right select
+> select #1/A:442
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> hide sel pseudobonds
+> select #1/A:960@N1
+atom, 1 residue, 1 model selected
+> select #1/A:442@C
+atom, 1 residue, 1 model selected
+> select #1/A:960@N1
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> distance #2/B:528@O #1/A:442@C
+Distance between PKS13-dimer-fit172-coot.pdb #2/B PHE 528 O and 2qo3 KS3AT3
+cerulenin.pdb #1/A PHE 442 C: 1.506Å
+> undo
+> ui mousemode right distance
+> ~distance #2/B:528@O #1/A:442@C
+> ~distance #1/A:442@C #1/A:960@N1
+> distance #1/A:442@C #1/A:960@N1
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A PHE 442 C and CER 960 N1:
+.373Å
+> ui mousemode right select
+> select #1/A:442
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> select #2/B:528@CA
+atom, 1 residue, 1 model selected
+> show sel cartoons
+> ui mousemode right distance
+> save "/Users/sarah/Documents/Work/PKS13/Pks13 cerulin platensimycin.pdb"
+> ui mousemode right distance
+> undo
+> distance #1/A:960@N1 #2/B:463@NE2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 N1 and PKS13-dimer-
+fit172-coot.pdb #2/B HIS 463 NE2: 4.989Å
+> distance #2/B:463@NE2 #1/A:960@O2
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2 and 2qo3 KS3AT3
+cerulenin.pdb #1/A CER 960 O2: 2.861Å
+> ~distance #1/A:960@N1 #2/B:463@NE2
+> distance #1/A:960@O2 #1/A:337@NE2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 O2 and HIS 337 NE2:
+.382Å
+> distance #1/A:337@NE2 #1/A:377@NE2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A HIS 337 NE2 and HIS 377 NE2:
+.050Å
+> distance #1/A:377@NE2 #1/A:960@O2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A HIS 377 NE2 and CER 960 O2:
+.748Å
+> ~distance #1/A:337@NE2 #1/A:377@NE2
+> ~distance #2/B:463@NE2 #1/A:960@O2
+> distance #1/A:960@O2 #2/B:463@NE2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 O2 and PKS13-dimer-
+fit172-coot.pdb #2/B HIS 463 NE2: 2.861Å
+> ui mousemode right select
+> ui tool show "Color Actions"
+> color #3 #65f39dff models
+> undo
+> redo
+> color #3 #edef3bff models
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> ui tool show "Color Actions"
+> color #3 #5cef9dff models
+> undo
+> color #3 #87ec35ff models
+> color #3 #a9ec3dff models
+> color #3 #acec42ff models
+> color #3 #beec65ff models
+> color #3 #e3ec56ff models
+> select #2/B
+atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
+> ui tool show "Color Actions"
+> hide #!1 models
+> show #!1 models
+> color #3 #5ced9bff models
+> ui mousemode right distance
+> distance #2/B:463@NE2 #1/A:377@NE2
+Distance between PKS13-dimer-fit172-coot.pdb #2/B HIS 463 NE2 and 2qo3 KS3AT3
+cerulenin.pdb #1/A HIS 377 NE2: 0.411Å
+> distance #1/A:377@NE2 #1/A:960@O2
+Distance already exists; modify distance properties with 'distance style'
+> ~distance #1/A:377@NE2 #1/A:960@O2
+> distance #1/A:377@NE2 #1/A:960@O2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A HIS 377 NE2 and CER 960 O2:
+.748Å
+> distance #1/A:960@O2 #1/A:337@NE2
+Distance already exists; modify distance properties with 'distance style'
+> ~distance #1/A:960@O2 #1/A:337@NE2
+> ~distance #4/A:1001@O33 #4/A:303@NE2
+> distance #1/A:337@NE2 #1/A:960@O2
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A HIS 337 NE2 and CER 960 O2:
+.382Å
+> ~distance #1/A:442@C #1/A:960@N1
+> distance #1/A:960@O2 #1/A:960@N1
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 O2 and N1: 2.254Å
+> distance #1/A:960@N1 #2/B:528@O
+Distance already exists; modify distance properties with 'distance style'
+> ~distance #1/A:960@O2 #1/A:960@N1
+> ui mousemode right select
+> select #1/A:442
+atoms, 11 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #1/A:960@N1
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> select clear
+> distance #1/A:960@N1 #1/A:442@C
+Distance between 2qo3 KS3AT3 cerulenin.pdb #1/A CER 960 N1 and PHE 442 C:
+.373Å
+> ui mousemode right select
+> show sel cartoons
+> select clear
+> save /Users/sarah/Desktop/image18.png supersample 3
+> lighting simple
+> lighting full
+> save /Users/sarah/Desktop/image19.png supersample 3
+> graphics silhouettes true
+> graphics silhouettes false
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes true
+> save /Users/sarah/Desktop/image20.png supersample 3
+> select add #2
+atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 6 models selected
+> show sel surfaces
+> select clear
+Drag select of PKS13-dimer-fit172-coot.pdb_B SES surface, 891 of 707554
+triangles, cap far, 60 of 8194 triangles, 6 atoms, 16 residues, 8 bonds, 1
+pseudobonds
+Drag select of PKS13-dimer-fit172-coot.pdb_B SES surface, 412 of 707554
+triangles, cap far, 56 of 8389 triangles, 5 residues
+> ui mousemode right translate
+> save /Users/sarah/Desktop/image21.png supersample 3
+> lighting full
+> lighting simple
+> lighting full
+> lighting flat
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> save /Users/sarah/Desktop/image22.png supersample 3
+> close
+> open "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"
+Chain information for
+test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1
+---
+Chain | Description
+A B | No description available
+> select
+atoms, 1028 bonds, 140 residues, 1 model selected
+> color sel cornflower blue
+> color sel blue
+> ui tool show "Color Actions"
+> color sel royal blue target p
+> ui tool show "Color Actions"
+> color sel royal blue target p
+> color sel royal blue target acspfl
+> select clear
+> ui mousemode right zoom
+> preset "overall look" "publication 1 (silhouettes)"
+Using preset: Overall Look / Publication 1 (Silhouettes)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes t
+    lighting depthCue f
+> preset "overall look" "publication 2 (depth-cued)"
+Using preset: Overall Look / Publication 2 (Depth-Cued)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes f
+    lighting depthCue t
+> ui mousemode right translate
+> ui mousemode right zoom
+> save "/Users/sarah/Documents/Work/PKS13/DH AlphaFold/DH.jpg" width 3000
+> height 1619 supersample 3
+> save "/Users/sarah/Documents/Work/PKS13/DH AlphaFold/DH.gif" width 4000
+> height 2158 supersample 3
+> save "/Users/sarah/Documents/Work/PKS13/DH AlphaFold/DH.tif" width 5000
+> height 2698 supersample 3 transparentBackground true
+> open
+> /Users/sarah/Documents/Work/PKS13/ACP/test_8ce23_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+test_8ce23_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #2
+---
+Chain | Description
+A | No description available
+> close #1
+> select
+atoms, 601 bonds, 74 residues, 1 model selected
+> color sel orange
+> ui tool show "Color Actions"
+> color sel dark orange target acspfl
+> select clear
+> preset "overall look" "publication 2 (depth-cued)"
+Using preset: Overall Look / Publication 2 (Depth-Cued)
+Preset expands to these ChimeraX commands:
+    set bg white
+    graphics silhouettes f
+    lighting depthCue t
+> ui tool show "Show Sequence Viewer"
+> sequence chain /A
+Alignment identifier is 2/A
+> select /A:2-13,17-19,26-29,33-46,54-56,62-73
+atoms, 377 bonds, 48 residues, 1 model selected
+> select /A:33
+atoms, 5 bonds, 1 residue, 1 model selected
+> select /A:33
+atoms, 5 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> ui mousemode right select
+> select /A:33
+atoms, 5 bonds, 1 residue, 1 model selected
+> color sel byhetero
+> select clear
+> save "/Users/sarah/Documents/Work/PKS13/DH AlphaFold/ACP2.tif" width 4000
+> height 2158 supersample 3
+> save "/Users/sarah/Documents/Work/PKS13/DH AlphaFold/ACP2.tif" width 5000
+> height 2698 supersample 3 transparentBackground true
+> close
+> open "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb"
+Chain information for
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #1
+---
+Chain | Description
+A B | No description available
+> open "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb"
+> "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb"
+> "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb"
+> "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb"
+> "/Users/sarah/Documents/Work/PKS13/DH
+> AlphaFold/test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"
+Chain information for
+test_cd2bf_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb #2
+---
+Chain | Description
+A B | No description available
+Chain information for
+test_cd2bf_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb #3
+---
+Chain | Description
+A B | No description available
+Chain information for
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb #4
+---
+Chain | Description
+A B | No description available
+Chain information for
+test_cd2bf_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #5
+---
+Chain | Description
+A B | No description available
+Chain information for
+test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #6
+---
+Chain | Description
+A B | No description available
+> ui tool show Matchmaker
+> matchmaker #2 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
+chain A (#1) with
+test_cd2bf_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb,
+chain A (#2), sequence alignment score = 347.5
+RMSD between 66 pruned atom pairs is 0.893 angstroms; (across all 70 pairs:
+.070)
+> matchmaker #3 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
+chain A (#1) with
+test_cd2bf_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb,
+chain A (#3), sequence alignment score = 353.5
+RMSD between 70 pruned atom pairs is 0.587 angstroms; (across all 70 pairs:
+.587)
+> matchmaker #4 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
+chain A (#1) with
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
+chain A (#4), sequence alignment score = 353.5
+RMSD between 70 pruned atom pairs is 0.000 angstroms; (across all 70 pairs:
+.000)
+> matchmaker #5 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
+chain A (#1) with
+test_cd2bf_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb,
+chain A (#5), sequence alignment score = 353.5
+RMSD between 69 pruned atom pairs is 0.714 angstroms; (across all 70 pairs:
+.784)
+> matchmaker #6 to #1
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker
+test_cd2bf_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
+chain A (#1) with
+test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
+chain A (#6), sequence alignment score = 353.5
+RMSD between 67 pruned atom pairs is 0.672 angstroms; (across all 70 pairs:
+.854)
+No reference and/or match structure/chain chosen
+> close
+> open "/Users/sarah/Documents/Work/PKS13/Pks13 cerulin platensimycin.pdb"
+> format pdb
+Summary of feedback from opening /Users/sarah/Documents/Work/PKS13/Pks13
+cerulin platensimycin.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 48
+GLU A 58 1 11
+Start residue of secondary structure not found: HELIX 2 2 ASP A 73 HIS A 78 1
+Start residue of secondary structure not found: HELIX 3 3 ASP A 103 GLY A 108
+6
+Start residue of secondary structure not found: HELIX 4 4 SER A 110 ALA A 116
+7
+End residue of secondary structure not found: HELIX 5 5 ASP A 118 ALA A 135 1
+Start residue of secondary structure not found: HELIX 6 6 ASP A 138 ARG A 143
+6
+Start residue of secondary structure not found: HELIX 7 7 GLY A 170 GLY A 175
+6
+Start residue of secondary structure not found: HELIX 8 8 ALA A 177 GLY A 190
+14
+Start residue of secondary structure not found: HELIX 9 9 THR A 200 CYS A 202
+3
+Start residue of secondary structure not found: HELIX 10 10 SER A 203 LYS A
+1 16
+messages similar to the above omitted
+End residue of secondary structure not found: HELIX 18 18 ALA A 381 GLY A 397
+17
+Start residue of secondary structure not found: HELIX 19 19 SER A 480 LEU A
+1 16
+Start residue of secondary structure not found: HELIX 21 21 THR A 526 GLY A
+1 15
+Start residue of secondary structure not found: HELIX 22 22 GLY A 574 SER A
+1 7
+Start residue of secondary structure not found: HELIX 23 23 SER A 581 MET A
+1 15
+Start residue of secondary structure not found: HELIX 24 24 ALA A 596 GLN A
+1 4
+messages similar to the above omitted
+End residue of secondary structure not found: HELIX 29 29 GLY A 695 ARG A 702
+8
+Start residue of secondary structure not found: HELIX 30 30 LEU A 703 GLN A
+1 5
+Start residue of secondary structure not found: HELIX 31 31 GLU A 726 ALA A
+1 13
+End residue of secondary structure not found: HELIX 32 32 SER A 755 GLU A 759
+5
+Start residue of secondary structure not found: HELIX 33 33 VAL A 761 GLY A
+1 10
+Start residue of secondary structure not found: HELIX 34 34 ASP A 791 LEU A
+1 5
+Start residue of secondary structure not found: HELIX 35 35 ASP A 796 GLU A
+1 11
+End residue of secondary structure not found: HELIX 36 36 PHE A 810 SER A 820
+11
+Start residue of secondary structure not found: HELIX 37 37 VAL A 834 GLU A
+1 11
+Start residue of secondary structure not found: HELIX 38 38 GLY A 862 VAL A
+1 15
+Start residue of secondary structure not found: HELIX 39 39 ARG A 882 LEU A
+1 6
+Start residue of secondary structure not found: HELIX 40 40 LEU B 42 VAL B 46
+5
+Start residue of secondary structure not found: HELIX 41 41 THR B 48 GLU B 58
+11
+Start residue of secondary structure not found: HELIX 42 42 ASP B 73 HIS B 78
+6
+messages similar to the above omitted
+End residue of secondary structure not found: HELIX 45 45 ASP B 118 ALA B 135
+18
+Start residue of secondary structure not found: HELIX 46 46 ASP B 138 ARG B
+1 6
+Start residue of secondary structure not found: HELIX 47 47 GLY B 170 GLY B
+1 6
+Start residue of secondary structure not found: HELIX 48 48 ALA B 177 GLY B
+1 14
+Start residue of secondary structure not found: HELIX 49 49 THR B 200 CYS B
+1 3
+Start residue of secondary structure not found: HELIX 50 50 SER B 203 LYS B
+1 16
+messages similar to the above omitted
+End residue of secondary structure not found: HELIX 58 58 ALA B 381 GLY B 397
+17
+Start residue of secondary structure not found: HELIX 59 59 SER B 480 GLU B
+1 17
+Start residue of secondary structure not found: HELIX 61 61 THR B 526 ALA B
+1 14
+Start residue of secondary structure not found: HELIX 62 62 GLY B 574 SER B
+1 7
+Start residue of secondary structure not found: HELIX 63 63 SER B 581 ALA B
+1 16
+Start residue of secondary structure not found: HELIX 64 64 LYS B 602 GLN B
+1 8
+Start residue of secondary structure not found: HELIX 65 65 ARG B 618 TYR B
+1 23
+messages similar to the above omitted
+End residue of secondary structure not found: HELIX 68 68 GLY B 695 LEU B 703
+9
+Start residue of secondary structure not found: HELIX 69 69 GLU B 726 ASP B
+1 11
+Start residue of secondary structure not found: HELIX 70 70 CYS B 737 ILE B
+1 6
+End residue of secondary structure not found: HELIX 71 71 SER B 755 ARG B 760
+6
+Start residue of secondary structure not found: HELIX 72 72 VAL B 761 GLY B
+1 10
+Start residue of secondary structure not found: HELIX 73 73 ASP B 791 LEU B
+1 5
+Start residue of secondary structure not found: HELIX 74 74 ASP B 796 GLU B
+1 11
+Start residue of secondary structure not found: HELIX 75 75 ARG B 809 SER B
+1 12
+Start residue of secondary structure not found: HELIX 76 76 VAL B 834 GLU B
+1 11
+messages similar to the above omitted
+End residue of secondary structure not found: SHEET 5 5 1 GLY A 148 GLY A 152
+Start residue of secondary structure not found: SHEET 6 6 1 SER A 195 ASP A
+0
+Start residue of secondary structure not found: SHEET 7 7 1 ALA A 224 ALA A
+0
+Start residue of secondary structure not found: SHEET 8 8 1 GLY A 268 ARG A
+0
+Start residue of secondary structure not found: SHEET 9 9 1 ALA A 289 GLN A
+0
+Start residue of secondary structure not found: SHEET 10 10 1 ALA A 333 GLU A
+0
+messages similar to the above omitted
+End residue of secondary structure not found: SHEET 19 19 1 VAL A 547 VAL A
+0
+Start residue of secondary structure not found: SHEET 20 20 1 VAL A 559 PHE A
+0
+Start residue of secondary structure not found: SHEET 21 21 1 ALA A 646 GLY A
+0
+Start residue of secondary structure not found: SHEET 23 23 1 ALA A 714 GLY A
+0
+Start residue of secondary structure not found: SHEET 24 24 1 SER A 720 GLY A
+0
+Start residue of secondary structure not found: SHEET 25 25 1 THR A 780 HIS A
+0
+messages similar to the above omitted
+End residue of secondary structure not found: SHEET 35 35 1 GLY B 148 GLY B
+0
+Start residue of secondary structure not found: SHEET 36 36 1 SER B 195 ASP B
+0
+Start residue of secondary structure not found: SHEET 37 37 1 ALA B 224 ALA B
+0
+Start residue of secondary structure not found: SHEET 38 38 1 GLY B 268 ARG B
+0
+Start residue of secondary structure not found: SHEET 39 39 1 ALA B 289 GLN B
+0
+Start residue of secondary structure not found: SHEET 40 40 1 ALA B 333 GLU B
+0
+messages similar to the above omitted
+End residue of secondary structure not found: SHEET 49 49 1 VAL B 547 VAL B
+0
+Start residue of secondary structure not found: SHEET 50 50 1 VAL B 559 PHE B
+0
+Start residue of secondary structure not found: SHEET 51 51 1 ALA B 646 GLY B
+0
+Start residue of secondary structure not found: SHEET 53 53 1 ALA B 714 GLY B
+0
+Start residue of secondary structure not found: SHEET 54 54 1 SER B 720 GLY B
+0
+End residue of secondary structure not found: SHEET 55 55 1 VAL B 744 ASP B
+0
+Start residue of secondary structure not found: SHEET 56 56 1 THR B 780 PHE B
+0
+Start residue of secondary structure not found: SHEET 57 57 1 ALA B 824 GLU B
+0
+Start residue of secondary structure not found: SHEET 58 58 1 VAL B 852 VAL B
+0
+Start residue of secondary structure not found: SHEET 59 59 1 LYS B 903 ARG B
+0
+Start residue of secondary structure not found: HELIX 1 1 THR A 48 GLU A 58 1
+messages similar to the above omitted
+End residue of secondary structure not found: SHEET 4 4 1 GLY A 101 PHE A 102
+Start residue of secondary structure not found: SHEET 5 5 1 GLY A 148 GLY A
+0
+Start residue of secondary structure not found: SHEET 6 6 1 SER A 195 ASP A
+0
+Start residue of secondary structure not found: SHEET 7 7 1 ALA A 224 ALA A
+0
+Start residue of secondary structure not found: SHEET 8 8 1 GLY A 268 ARG A
+0
+[deleted to fit within ticket limits]
 Start residue of secondary structure not found: SHEET 9 9 1 ALA A 289 GLN A
 0