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Changes between Initial Version and Version 1 of Ticket #18644

Timestamp:: Aug 27, 2025, 5:50:13 PM (8 weeks ago)
Author:: pett
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #18644
- Property Component Unassigned → Sessions
- Property Owner set to pett
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → accepted
- Property Summary ChimeraX bug report submission → Combining sessions error if global pseudobond groups in both

Ticket #18644 – Description

-              initial
+              v1
 > select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> select add #2/B:336@O
+atoms, 2 residues, 1 model selected
+> select add #2/B:327@O
+atoms, 3 residues, 1 model selected
+> select up
+atoms, 3 bonds, 3 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6553 bonds, 16 pseudobonds, 522 residues, 3 models selected
+> style sel ball
+Changed 6585 atom styles
+> style sel stick
+Changed 6585 atom styles
+> style sel ball
+Changed 6585 atom styles
+> style sel stick
+Changed 6585 atom styles
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_3_highres.tif" width 1421 height 1080 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active stie.cxs"
+> select clear
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel bgColor whitw
+Invalid "bgColor" argument: Expected 'none' or a color
+> label sel bgColor white
+> select #2/B:143@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 16 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> label sel bgColor none
+> label sel height fixed
+> label sel defaultHeight
+Missing "defaultHeight" keyword's argument
+> label sel height defaultHeight
+Invalid "height" argument: Expected 'fixed' or a number
+> label sel height default
+Invalid "height" argument: Expected 'fixed' or a number
+> label sel height 0
+> label sel height 2
+> label sel height 1
+> label sel height 0.5
+> label sel height 0.6
+> label sel height 0.7
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel size 40
+> label sel size 42
+> label sel size 48
+> label sel size 30
+> label sel size 48
+> label sel height 0.5
+> label sel height 0.6
+> select clear
+> select #2/B:159@OD2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel height 0.65
+> select clear
+> select #2/B:144
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel #ee8fff7f target cspf
+> color sel #ee8fff77 target cspf
+> color sel #ee8fff00 target cspf
+> color sel #ee8fff01 target cspf
+> color sel #ee8fff04 target cspf
+> color sel #ee8fffff target cspf
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_3_highres.tif" width 1421 height 1080 supersample 4
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active stie.cxs"
+> help help:user
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting fillDirection 0.2,-0.2-,-0.959
+Invalid "fillDirection" argument: Expected a number
+> lighting fillDirection 0.2,-0.2,-0.959
+> lighting fillDirection -0.2,-0.2,-0.959
+> lighting fillDirection 0.2,-0.2,-0.959
+> lighting fillDirection -0.2,-0.2,-0.959
+> lighting fillDirection -0.2,0.2,-0.959
+> lighting fillDirection -0.2,-0.2,-0.959
+> lighting fillDirection -0.2,0.1,-0.959
+> lighting fillDirection -0.3,0.1,-0.959
+> lighting fillDirection -0.2,0.1,-0.959
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+——— End of log from Mon Apr 21 17:37:05 2025 ———
+opened ChimeraX session
+> view active-site-1
+Expected an objects specifier or a view name or a keyword
+> view list
+Named views: active-site, active-site-2, active-site-3
+> view active-site-3
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> label sel offset 0,0,0
+> label sel offset 0,0,5
+[Repeated 1 time(s)]
+> label sel offset 0,5,5
+> label sel offset 5,5,5
+> label sel offset 0,5,5
+> label sel offset 0,0,5
+> label sel offset 0,2,5
+[Repeated 1 time(s)]
+> label sel offset 0,2,10
+> label sel offset 0-2,2,7
+Invalid "offset" argument: Expected 'default' or 3-tuple of numbers
+> label sel offset -2,2,7
+> select clear
+> label sel bgColor white
+> select #2/B:159@OD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> select clear
+> color #3 #00fdffff models
+> select clear
+> select add #4.2
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 3 models selected
+> select add #2
+atoms, 13112 bonds, 27 pseudobonds, 1050 residues, 7 models selected
+> color sel #F187EE
+> color sel byhetero
+> select subtract #2
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 3 models selected
+> color sel #BF87F1
+> color sel byhetero
+> select clear
+> color #3 #00f900ff models
+> color #3 #00fdffff models
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> color sel hot pink
+> color #2 #87F18B
+> view name active-site-1
+> color #4.2 #87F1C0
+> color #2,4.2 byhetero
+> color #2 byhetero
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> color sel hot pink
+> select clear
+> color #3 #00fdffff models
+> select clear
+> color #2.2 #00fdffff models
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> label sel text Mn(III)
+> select #2/B:143@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 16 bonds, 1 residue, 1 model selected
+> label sel height 0.7
+> label sel height 0.5
+> label sel height 0.6
+> select clear
+> view name active-site-1
+> select $4.2/d
+Expected an objects specifier or a keyword
+> select #4.2/d
+Nothing selected
+> select #4.2/b
+atoms, 3284 bonds, 5 pseudobonds, 266 residues, 2 models selected
+> ui tool show "Change Chain IDs"
+> changechains sel D
+Chain IDs of 266 residues changed
+> select #4.2/D:166@CE1
+atom, 1 residue, 1 model selected
+> select add #4.2/D:162@DG2
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select clear
+[Repeated 1 time(s)]
+> select #2/B:26@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> select #2/B:74@ND1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 Active
+> site_3.cxs"
+——— End of log from Thu Apr 24 12:40:38 2025 ———
+opened ChimeraX session
+> color #3 deep sky blue type p
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color #3 deep sky blue target p
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_5_highres.tif" width 1173 height 1080 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox.cxs"
+——— End of log from Thu Apr 24 19:50:15 2025 ———
+opened ChimeraX session
+> close #1
+> rename #4 name MnSOD_ox id #1
+> rename #2 name MnSOD_ox id #1.1
+> rename #3 name ox__hbonds id #1.3
+> open 7kkw name MnSOD_red
+Summary of feedback from opening 7kkw fetched from pdb
+---
+warnings | Atom D1 is not in the residue template for MET /A:0
+Atom D is not in the residue template for LYS /A:1
+Atom D is not in the residue template for HIS /A:2
+Atom D is not in the residue template for SER /A:3
+Atom D is not in the residue template for LEU /A:4
+Atom DA is not in the residue template for PRO /A:5
+Atom D is not in the residue template for ASP /A:6
+Atom D is not in the residue template for LEU /A:7
+Atom DA is not in the residue template for PRO /A:8
+Too many hydrogens missing from residue template(s) to warn about
+MnSOD_red title:
+Neutron structure of Reduced Human MnSOD [more info...]
+Chain information for MnSOD_red #2
+---
+Chain | Description | UniProt
+A B | Superoxide dismutase [Mn], mitochondrial | SODM_HUMAN 1-198
+Non-standard residues in MnSOD_red #2
+---
+D8U — deuterium(1+)
+MN — manganese (II) ion
+MnSOD_red mmCIF Assemblies
+---
+| author_and_software_defined_assembly
+> sym # 2 assembly 1
+Made 2 copies for MnSOD_red assembly 1
+> close #2
+> rename #3 name MnSOD_red id #2
+> ui tool show Matchmaker
+> matchmaker #!2.1 to #1.1 bring #!2.2
+Computing secondary structure
+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 MnSOD_ox, chain B (#1.1) with MnSOD_red, chain A (#2.1), sequence
+alignment score = 1082.2
+RMSD between 198 pruned atom pairs is 0.261 angstroms; (across all 199 pairs:
+.320)
+> select #1 & @@display
+atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected
+> select #2 & #1 :<1
+atoms, 12752 bonds, 20 pseudobonds, 890 residues, 4 models selected
+> select #1 & @@display
+atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected
+> select #2 & sel :<1
+atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected
+> show sel atoms
+> name frozen sh-r sel
+> select #1 & @@display
+atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected
+> name frozen sh-o sel
+> select sh-r
+atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected
+> select sh-r
+atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected
+> hide #!1 models
+> select add #2.1/A:302@O
+atoms, 608 bonds, 20 pseudobonds, 49 residues, 4 models selected
+> select up
+atoms, 610 bonds, 20 pseudobonds, 49 residues, 4 models selected
+> select add #2.1/A:541@D
+atoms, 610 bonds, 20 pseudobonds, 50 residues, 4 models selected
+> name frozen sh-r sel
+> select #2.1/A:324@D1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> hide sel atoms
+> select #2.1/A:25
+atoms, 18 bonds, 1 residue, 1 model selected
+> hide #2 & backbone & ~CA
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> hide #2 & backbone & ~@CA
+> select clear
+> select #2.1/A:25
+atoms, 18 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2.1/A:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> select clear
+> cartoon #2 suppressBackboneDisplay false
+> hbonds #2 sh-r & ~backbond restrict #2 rev t interSubmodel t name red_hbonds
+Expected a keyword
+> hbonds sh-r & ~backbond restrict #2 rev t interSubmodel t name red_hbonds
+Expected a keyword
+> select sh-r & ~backbone
+atoms, 394 bonds, 20 pseudobonds, 50 residues, 4 models selected
+> hbonds sel restrict #2 reveal true interSubmodel true name red_hbonds
+hydrogen bonds found
+> select #2.1/A:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2.2/A:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select add #2.2/A:166
+atoms, 34 bonds, 2 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6489 bonds, 32 pseudobonds, 521 residues, 3 models selected
+> hide sel atoms
+> select #2.1/A:166
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #2.1/A:162
+atoms, 34 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> view active-site-1
+[Repeated 1 time(s)]
+> select #2.1/A:357@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2.1/A:338@O
+atom, 1 residue, 1 model selected
+> select add #2.1/A:326@O
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #2 & hbondatoms & @@display
+Nothing selected
+> select hbondatoms & @@display
+Nothing selected
+> select hbondatoms
+Nothing selected
+> select hbondatoms
+Nothing selected
+> select #2 & pbondatoms & @@display
+atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> select #2 & pbondatoms & @@display
+atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected
+> select clear
+> select add #3
+pseudobonds, 1 model selected
+> select up
+pseudobonds, 3 models selected
+> select up
+pseudobonds, 3 models selected
+> select up
+pseudobonds, 3 models selected
+> select up
+pseudobonds, 3 models selected
+> select down
+pseudobonds, 1 model selected
+> select down
+pseudobonds, 1 model selected
+> select clear
+> select #2 & pbondatoms & @@display
+atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected
+> select subtract #2.1/A:201@MN
+atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected
+> select subtract #2.1/A:26@NE2
+atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected
+> select subtract #2.1/A:163@NE2
+atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected
+> select subtract #2.1/A:317@O
+atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected
+> select subtract #2.1/A:74@NE2
+atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected
+> select subtract #2.1/A:30@NE2
+atoms, 1 bond, 24 pseudobonds, 28 residues, 4 models selected
+> select subtract #2.2/A:166@OH
+atoms, 1 bond, 23 pseudobonds, 27 residues, 4 models selected
+> select add #2.2/A:166@OH
+atoms, 1 bond, 23 pseudobonds, 28 residues, 4 models selected
+> hbonds sel restrict both reveal true interSubmodel true name red_hbonds
+hydrogen bonds found
+> select up
+atoms, 404 bonds, 5 pseudobonds, 28 residues, 3 models selected
+> hbonds sel restrict both interSubmodel true name red_hbonds
+hydrogen bonds found
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select clear
+> rename #3 id 2.3
+> select clear
+> ui tool show "Selection Inspector"
+> setattr sel g halfbond true
+Assigning halfbond attribute to 1 item
+> setattr sel g radius 0.155
+Assigning radius attribute to 1 item
+> style sel dashes 0
+Changed 1 pseudobond dash
+> select clear
+> select #2.1/A:317@O
+atom, 1 residue, 1 model selected
+> select add #2.1/A:501@D
+atoms, 2 residues, 1 model selected
+> pbond sel dashes 0 name shared-H
+> select subtract #2.1/A:501@D
+atom, 1 residue, 1 model selected
+> select #2.1/A:501@D
+atom, 1 residue, 1 model selected
+> select add #2.1/A:143@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel dashes 0 name shared-H
+> select #2.1/A:30@NE2
+atom, 1 residue, 1 model selected
+> select add #2.1/A:541@D
+atoms, 2 residues, 1 model selected
+> pbond sel dashes 0 name shared-H
+> select #2.1/A:541@D
+atom, 1 residue, 1 model selected
+> select add #2.2/A:166@OH
+atoms, 2 residues, 2 models selected
+> pbond sel dashes 0 name shared-H
+> combine #2.1.2#3 close true modelID 2.1.2
+Expected a keyword
+> combine #2.1.2#3 close true modelId 2.1.2
+No structures specified
+> select add #2.1.2
+atoms, 3 pseudobonds, 2 residues, 3 models selected
+> select add #3
+atoms, 4 pseudobonds, 2 residues, 4 models selected
+> select add #2.1
+atoms, 6523 bonds, 33 pseudobonds, 524 residues, 6 models selected
+> select subtract #2.1
+atom, 1 residue, 1 model selected
+> select add #2.2
+atoms, 6523 bonds, 12 pseudobonds, 523 residues, 3 models selected
+> select subtract #2.2
+Nothing selected
+> select add #2.1.2
+pseudobonds, 1 model selected
+> select add #3
+pseudobonds, 2 models selected
+> combine sel close true modelId 2.1.2
+No structures specified
+> select clear
+> rename #3 id #2.1.2
+> undo2
+Unknown command: undo2
+> undo
+> select subtract #2.1.2.1
+pseudobonds, 1 model selected
+> select add #2.1.2.1
+pseudobonds, 2 models selected
+> hide #2.1.2.1 models
+> show #2.1.2.1 models
+> ui tool show "Selection Inspector"
+> setattr sel g halfbond true
+Assigning halfbond attribute to 2 items
+> select clear
+> select #2 & pbondatoms & backbone
+atoms, 3 pseudobonds, 12 residues, 3 models selected
+> select up
+atoms, 189 bonds, 3 pseudobonds, 12 residues, 3 models selected
+> select down
+atoms, 3 pseudobonds, 12 residues, 3 models selected
+> select #2 & sel @<1
+atoms, 3 pseudobonds, 12 residues, 3 models selected
+> select #2 & sel @<1.5
+atoms, 12 bonds, 3 pseudobonds, 12 residues, 3 models selected
+> select ~sel & ::selected & ~sidechain
+atoms, 13 bonds, 12 residues, 2 models selected
+> hide sel atoms
+> hide @DA
+> ui tool show "Selection Inspector"
+> setattr =sel b display false
+Assigning display attribute to 5 items
+> select #2.1/A:70@DA3
+atom, 1 residue, 1 model selected
+> select add #2.1/A:70@DA2
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view active-site-1
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:143@O
+atom, 1 residue, 1 model selected
+> select add #2.1/A:143@C
+atoms, 1 residue, 1 model selected
+> select add #2.1/A:163@D
+atoms, 2 residues, 1 model selected
+> select add #2.1/A:163@N
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> select #2.1/A:302@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select add #2.1/A:142@O
+atoms, 2 bonds, 2 residues, 1 model selected
+> select up
+atoms, 15 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> show #!1 models
+> hide #!1 models
+> undo
+[Repeated 4 time(s)]
+> select clear
+> select #2.1/A:29
+atoms, 21 bonds, 1 residue, 1 model selected
+> select add #2.1/A:28
+atoms, 31 bonds, 2 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr sel r ss_type 1
+Assigning ss_type attribute to 2 items
+> setattr sel r ss_type 0
+Assigning ss_type attribute to 2 items
+> setattr sel r ss_type 1
+Assigning ss_type attribute to 2 items
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+——— End of log from Fri Apr 25 13:02:38 2025 ———
+opened ChimeraX session
+> select #2.1/A:142
+atoms, 13 bonds, 1 residue, 1 model selected
+> select clear
+> select #2.1/A:501@D
+atom, 1 residue, 1 model selected
+> select add #2.1/A:317@O
+atoms, 2 residues, 1 model selected
+> select add #2.1/A:330@O
+atoms, 3 residues, 1 model selected
+> select add #2.1/A:541@D
+atoms, 4 residues, 1 model selected
+> select up
+atoms, 3 bonds, 4 residues, 1 model selected
+> style sel ball
+Changed 7 atom styles
+> select clear
+> select #2.1/A:541@D
+atom, 1 residue, 1 model selected
+> style sel stick
+Changed 1 atom style
+> style sel ball
+Changed 1 atom style
+> select clear
+> color #2.1 & C #59ECA9 target abrs
+> color #2.2 & C #59E6EC target abrs
+> select clear
+> view active-site-1
+> select #2.1/A:161@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> select intersect sidechain
+atoms, 21 bonds, 1 residue, 1 model selected
+> lighting flat
+> color sel #67ffc4ff target af
+[Repeated 3 time(s)]
+> color sel #59eca9ff target af
+> color sel #59ecaaff target af
+[Repeated 3 time(s)]
+> color sel #59eca9ff target af
+> color sel #59ecaaff target af
+[Repeated 2 time(s)]
+> color sel #59edabff target af
+[Repeated 2 time(s)]
+> color sel #59eca9ff target af
+[Repeated 1 time(s)]
+> color sel #59edaaff target af
+> color sel #5aedaaff target af
+> color sel #5aedabff target af
+[Repeated 1 time(s)]
+> color sel #8affa1ff target af
+> color sel #94c5a9ff target af
+> color sel #8cf8a3ff target af
+> color sel #95c1a8ff target af
+[Repeated 1 time(s)]
+> color sel #59eca9ff target af
+[Repeated 1 time(s)]
+> color sel #59eca9fa target af
+> color sel #59eca9f4 target af
+> color sel #59eca9e8 target af
+> color sel #59eca9d0 target af
+> color sel #59eca9ca target af
+> color sel #59eca9c7 target af
+> color sel #59eca9c2 target af
+> color sel #59eca9bd target af
+> color sel #59eca9b6 target af
+> color sel #59eca9ae target af
+> color sel #59eca9ab target af
+> color sel #59eca9a8 target af
+> color sel #59eca9a5 target af
+> color sel #59eca9a0 target af
+> color sel #59eca99e target af
+> color sel #59eca99d target af
+> color sel #59eca99b target af
+[Repeated 1 time(s)]
+> color sel #59eca99a target af
+[Repeated 1 time(s)]
+> color sel #59eca99b target af
+[Repeated 1 time(s)]
+> color sel #59eca99c target af
+[Repeated 2 time(s)]
+> color sel #59eca99d target af
+[Repeated 1 time(s)]
+> color sel #59eca99c target af
+> color sel #59eca99b target af
+> color sel #59eca998 target af
+> color sel #59eca996 target af
+> color sel #59eca98f target af
+> color sel #59eca98c target af
+> color sel #59eca985 target af
+> color sel #59eca980 target af
+> color sel byhetero target af
+> color sel #59eca97f target af
+> color sel #59eca973 target af
+> color sel #59eca968 target af
+> color sel #59eca960 target af
+> color sel #59eca958 target af
+> color sel #59eca953 target af
+> color sel #59eca950 target af
+> color sel #59eca946 target af
+> color sel #59eca943 target af
+> color sel #59eca93c target af
+> color sel #59eca939 target af
+> color sel #59eca933 target af
+> color sel #59eca92e target af
+> color sel #59eca92a target af
+> color sel #59eca929 target af
+> color sel #59eca927 target af
+> color sel #59eca926 target af
+[Repeated 1 time(s)]
+> color sel #59eca925 target af
+> color sel #59eca926 target af
+[Repeated 1 time(s)]
+> color sel #59eca927 target af
+[Repeated 2 time(s)]
+> color sel #59eca928 target af
+> color sel #59eca929 target af
+> color sel #59eca92b target af
+> color sel #59eca930 target af
+> color sel #59eca937 target af
+> color sel #59eca93b target af
+> color sel #59eca947 target af
+> color sel #59eca94f target af
+> color sel #59eca957 target af
+> color sel #59eca961 target af
+> color sel #59eca968 target af
+> color sel #59eca96f target af
+> color sel #59eca974 target af
+> color sel #59eca978 target af
+> color sel #59eca979 target af
+> color sel #59eca97a target af
+> color sel #59eca97d target af
+> color sel #59eca980 target af
+> color sel #59eca989 target af
+> color sel #59eca99e target af
+> color sel #59eca9ed target af
+> color sel #59eca9ff target af
+> color sel #59eca9ef target af
+> color sel #59eca9d9 target af
+> color sel #59eca9b0 target af
+> color sel #59eca9a1 target af
+> color sel #59eca992 target af
+> color sel #59eca97a target af
+> color sel #59eca976 target af
+> color sel #59eca972 target af
+> color sel #59eca96d target af
+> color sel #59eca96b target af
+> color sel #59eca96a target af
+[Repeated 1 time(s)]
+> color sel #59eca96b target af
+[Repeated 1 time(s)]
+> color sel #59eca96c target af
+> color sel #59eca96d target af
+> color sel #59eca96e target af
+[Repeated 1 time(s)]
+> color sel #59eca96f target af
+[Repeated 1 time(s)]
+> color sel #59eca970 target af
+> color sel #59eca971 target af
+> color sel #59eca973 target af
+> color sel #59eca976 target af
+> color sel #59eca977 target af
+> color sel #59eca97a target af
+> color sel #59eca97d target af
+> color sel #59eca980 target af
+> color sel byhetero target af
+> select clear
+> view active-site-1
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> view active-site-1
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select #1.1/B:143@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 16 bonds, 1 residue, 1 model selected
+> select & sidechain
+Expected an objects specifier or a keyword
+> select sel & sidechain
+atoms, 12 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #1.1/B:143@DA
+atom, 1 residue, 1 model selected
+> hide sel cartoons
+> view active-site-1
+> select clear
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select #1.1/B:144
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #1.1/B:143@CB
+atom, 1 residue, 1 model selected
+> show sel cartoons
+> select #1.1/B:143@DA
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view active-site-1
+[Repeated 1 time(s)]
+> select C & @@displayed
+Nothing selected
+> select C
+atoms, 6544 bonds, 1592 residues, 4 models selected
+> select C & @@display
+atoms, 292 bonds, 60 residues, 4 models selected
+> select @D* & ((C & @@displayed) @:< 1.5)
+Expected a keyword
+> select (C & @@displayed) @:< 1.5
+Expected a keyword
+> select @D* & ((C & @@displayed) @< 1.5)
+Nothing selected
+> select (C & @@displayed) @< 1.5
+Nothing selected
+> select C & @@displayed
+Nothing selected
+> select @D* & ((C & @@display) @< 1.5)
+atoms, 84 residues, 4 models selected
+> hide sel & #!1.1-2 atoms
+> select clear
+> view active-site-1
+> select @D* & ((C & @@display) @< 1.5)
+atoms, 84 residues, 4 models selected
+> name "carbon Ds" @D* & ((C & @@display) @< 1.5)
+Not registering illegal selector name "carbon Ds"
+> name CDs @D* & ((C & @@display) @< 1.5)
+> select clear
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site-1
+> view active-site-3
+> view active-site
+> view active-site-3
+> view active-site-1
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel bgColor nonw
+Invalid "bgColor" argument: Expected 'none' or a color
+> label sel bgColor none
+> select clear
+> view active-site-1
+[Repeated 1 time(s)]
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox_no-CDs.tif"
+> width 1424 height 1080 supersample 4
+> view name active-site
+> show #!2 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide CDs
+> show CDs
+> hide CDs & (@DA | :GLY)
+> select clear
+> view active-site
+> select :* & @@display & ~backbone
+atoms, 659 bonds, 51 pseudobonds, 97 residues, 11 models selected
+> select #2:* & @@display & ~backbone
+atoms, 278 bonds, 24 pseudobonds, 48 residues, 6 models selected
+> label (#!2.1-2 & sel) text "{0.name} {0.number}{0.insertion_code}"
+> label (#!2.1-2 & sel) text "{0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select #2.3:* & @@display & ~backbone
+Nothing selected
+> select #2.2:* & @@display & ~backbone
+atoms, 22 bonds, 17 residues, 1 model selected
+> ~label sel residues
+> select #2.2/A:166@CD1
+atom, 1 residue, 1 model selected
+> select add #2.2/A:162@CG
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> ui tool show "Change Chain IDs"
+> select #2.2/a
+atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected
+> select add #2.2
+atoms, 6523 bonds, 12 pseudobonds, 523 residues, 4 models selected
+> select #2.2/a
+atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected
+> ui tool show "Change Chain IDs"
+> changechains sel D
+Chain IDs of 261 residues changed
+> select #2.2/d
+atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected
+> select #2.2/D:162@CG
+atom, 1 residue, 1 model selected
+> select add #2.2/D:166@CE1
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select #2.1/A:541@D
+atom, 1 residue, 1 model selected
+> select add #2.1/A:501@D
+atoms, 2 residues, 1 model selected
+> ~label sel residues
+> select #2.1/A:330@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text "WAT 2"
+> select #2.1/A:317@D1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel text "WAT 1"
+> label sel height 0.6
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3251 bonds, 261 residues, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> label sel text Mn(II)
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:330@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel height 0.6
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:143@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 15 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> show #!1 models
+> hide #!1 models
+> label sel bgColor white height 0.6
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> show #!1 models
+> hide #!1 models
+> hide #1.1.3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red.tif" width
+> 1117 height 1080 supersample 4
+> hide #!2 models
+> show #!1 models
+> show #1.1.3 models
+> hide #2.1.3 models
+> select #1.1/B:143@O
+atom, 1 residue, 1 model selected
+> select add #1.1/B:143@C
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view name active-site
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox.tif" width 1117
+> height 1080 supersample 4
+> hide CDs
+> show #2.1.3 models
+> hide #2.1.3 models
+> show #2.1.3 models
+> hide #2.2.2 models
+> hide #2.1.3 models
+> hide #!2 models
+> view active-site
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox_no-CDs.tif"
+> width 1117 height 1080 supersample 4
+> hide #1.1.3 models
+> hide #1.2.2 models
+> hide #!1 models
+> show #!2 models
+> show #2.1.3 models
+> show #2.2.2 models
+> select #2.1/A:165
+atoms, 21 bonds, 1 residue, 1 model selected
+> select add #2.1/A:166
+atoms, 41 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> view name active-site_red
+> select #2.1/A:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select up
+atoms, 68 bonds, 4 residues, 1 model selected
+> show sel cartoons
+> select up
+atoms, 3153 bonds, 199 residues, 1 model selected
+> show sel cartoons
+> select clear
+> select #2.1/A:74@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel bgColor none
+> select clear
+> view name active-site_red
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> label sel height 0.65
+> select clear
+> view name active-site_red
+> select clear
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> label sel height 0.7
+> select clear
+[Repeated 2 time(s)]
+> select #2.1/A:180
+atoms, 18 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select clear
+> view name active-site_red
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red_no-CDs_alt-
+> view.tif" width 1117 height 1080 supersample 4
+> view name active-site-1
+> view active-site
+> view active-site_red
+> hide #!2 models
+> show #!1 models
+> show #1.1.3 models
+> show #1.2.2 models
+> show #!2 models
+> hide #!2 models
+> view active-site_red
+> hide #!1 models
+> show #!2 models
+> hide #1.1.3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+——— End of log from Fri Apr 25 14:20:33 2025 ———
+opened ChimeraX session
+> select #2.1/b:34
+atoms, 20 bonds, 1 residue, 1 model selected
+> view sel
+> view active-site-3
+> select add #2.1/A:22
+atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected
+> select clear
+> select #2.1/A:22
+atoms, 18 bonds, 1 residue, 1 model selected
+> select clear
+[Repeated 2 time(s)]
+> select add #2.1.2
+pseudobonds, 2 models selected
+> style sel dashes 12
+Changed 2 pseudobond dashes
+> select clear
+> view active-site-3
+> select add #2.1.1
+pseudobonds, 1 model selected
+> select subtract #2.1.1
+Nothing selected
+> select add #2.1.2
+pseudobonds, 2 models selected
+> style sel dashes 10
+Changed 2 pseudobond dashes
+> select clear
+> select add #2.1.2
+pseudobonds, 2 models selected
+> style sel dashes 5
+Changed 2 pseudobond dashes
+> style sel dashes 2
+Changed 2 pseudobond dashes
+> style sel dashes 3
+Changed 2 pseudobond dashes
+> style sel dashes 4
+Changed 2 pseudobond dashes
+> style sel dashes 8
+Changed 2 pseudobond dashes
+> style sel dashes 12
+Changed 2 pseudobond dashes
+> style sel dashes 35
+Changed 2 pseudobond dashes
+> style sel dashes 20
+Changed 2 pseudobond dashes
+> style sel dashes 10
+Changed 2 pseudobond dashes
+> select clear
+> hide #2.1.3 models
+> show #2.1.3 models
+> hide #2.3 models
+> hide #2.1.3 models
+> show #2.1.3 models
+> show #2.3 models
+> hide #2.2.2 models
+> show CDs
+> show list
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> name list
+CDs @D* & ((C & @@display) @< 1.5)
+both_shell (ox_shell | red_shell)
+sh-o [482 atoms, 466 bonds, 5 models]
+sh-r [627 atoms, 610 bonds, 4 models]
+> hide @DA*
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+> combine #2 retainIds true
+'retainIds' requires residues number / insertion code combos be unique in each
+chain with the same ID (duplicate: /B MET 0)
+> combine #2 retainIds true modelId #3
+'retainIds' requires residues number / insertion code combos be unique in each
+chain with the same ID (duplicate: /B MET 0)
+> combine #2 modelId #3
+Remapping chain ID 'B' in MnSOD_red #2.2 to 'C'
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> select add #2
+atoms, 13046 bonds, 48 pseudobonds, 1046 residues, 10 models selected
+> select subtract #2
+Nothing selected
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #3.2 models
+> show #3.2 models
+> hide #3.2 models
+> show #3.2 models
+> hide #3.1 models
+> show #3.1 models
+> hide #!2.1 models
+> show #!2.1 models
+> hide #!2 models
+> hide #!3 models
+> show #!3 models
+> select add #3
+atoms, 13046 bonds, 25 pseudobonds, 1046 residues, 3 models selected
+> ui tool show "Change Chain IDs"
+> changechains sel D C
+Proposed chainID change conflicts with existing residue combination #3/C MET 0
+> changechains sel C,D D,C
+Chain IDs of 523 residues changed
+> select add #2.1
+atoms, 19569 bonds, 58 pseudobonds, 1569 residues, 9 models selected
+> select subtract #2.1
+atoms, 13046 bonds, 25 pseudobonds, 1046 residues, 3 models selected
+> show #!2 models
+> changechains #2.1 A,B B,A
+Chain IDs of 523 residues changed
+> select subtract #3
+Nothing selected
+> select add #3.1
+pseudobonds, 1 model selected
+> select subtract #3.1
+Nothing selected
+> hide #!3 models
+> show #!3 models
+> mcopy #2.1 toAtoms #3 settings csvlp
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #3.3 models
+> show #3.3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> view active-site-3
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> mcopy #2.1 toAtoms #3 settings csvly
+> mcopy #2.1 toAtoms #3 settings csvlxy
+> mcopy #2.1 toAtoms #3 settings csvlxpy
+> mcopy #2.1 toAtoms #3 settings csvlxp
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> close #3
+> show #!2 models
+> hide #2.3 models
+> show #2.3 models
+> changechains #2.1 A,B B,A
+Chain IDs of 523 residues changed
+> select add #2.2
+atoms, 6523 bonds, 12 pseudobonds, 523 residues, 4 models selected
+> ui tool show "Change Chain IDs"
+> select clear
+> hide #2.3 models
+> show #2.3 models
+> changechains #2.2 B,D D,C
+Chain IDs of 523 residues changed
+> select clear
+> combine #2 modelId #3
+> hide #3.1 models
+> show #3.1 models
+> hide #!2 models
+> hide #!3 models
+> show #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> ui tool show Matchmaker
+> matchmaker #3/B to #2.1/A pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MnSOD_red, chain A (#2.1) with combination, chain B (#3), sequence
+alignment score = 1082.8
+RMSD between 198 pruned atom pairs is 0.240 angstroms; (across all 199 pairs:
+.292)
+> show #!2 models
+> hide #!2 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_WIP.cxs"
+——— End of log from Fri Apr 25 16:51:41 2025 ———
+opened ChimeraX session
+> select #3/B:201@MN
+atom, 1 residue, 1 model selected
+> cofr sel
+> select #3/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #3/B:566@D
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> mcopy #2.1/a & protein toAtoms #3/b target csvl match f
+Expected a keyword
+> mcopy #2.1/a & protein toAtoms #3/b settings csvl matchResidues false
+> show #!2 models
+> hide #!2 models
+> mcopy #2.2/c toAtoms #3/d settings csvl matchResidues false
+> select add #3/D:166
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #3/D:162
+atoms, 34 bonds, 2 residues, 1 model selected
+> select up
+atoms, 191 bonds, 10 residues, 1 model selected
+> select up
+atoms, 3160 bonds, 199 residues, 1 model selected
+> select subtract #3/D:162
+atoms, 3144 bonds, 198 residues, 1 model selected
+> select subtract #3/D:166
+atoms, 3122 bonds, 197 residues, 1 model selected
+> hide sel atoms
+> select clear
+> ui mousemode right "move label"
+> hide #3/a,c
+> select clear
+> select #3/B:181
+atoms, 25 bonds, 1 residue, 1 model selected
+> select up
+atoms, 184 bonds, 10 residues, 1 model selected
+> show sel cartoons
+> select clear
+> hbonds #3 & @@display restrict both interModel false name red_hbonds
+hydrogen bonds found
+> delete sel
+> ~bond sel
+> delete pbonds sel
+[Repeated 1 time(s)]
+> select clear
+> select add #3/B:143@NE2
+atom, 1 bond, 1 residue, 1 model selected
+> pbond sel color deep sky blue name red_hbonds
+Must specify exactly 2 atoms to form pseudobond between; you specified 1
+> select #3/B:319@D2
+atom, 1 residue, 1 model selected
+> select add #3/B:143@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel color deep sky blue name red_hbonds
+Pseudobond group 'red_hbonds' already exists as a per-coordset group
+> pbond sel color deep sky blue
+> select clear
+> close #3.2
+> select #3/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #3/B:540@D
+atoms, 2 residues, 1 model selected
+> pbond sel name shared-H
+> select #3/B:30@NE2
+atom, 1 residue, 1 model selected
+> select #3/B:540@D
+atom, 1 residue, 1 model selected
+> select add #3/B:30@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel name shared-H
+> select add #3.2
+atoms, 2 pseudobonds, 2 residues, 2 models selected
+> ui tool show "Selection Inspector"
+> style sel dashes 10
+Changed 1 pseudobond dash
+> setattr sel g halfbond true
+Assigning halfbond attribute to 1 item
+> select add #3.1
+atoms, 24 pseudobonds, 2 residues, 3 models selected
+> select subtract #3.1
+atoms, 2 pseudobonds, 2 residues, 2 models selected
+> select add #3.1
+atoms, 24 pseudobonds, 2 residues, 3 models selected
+> select subtract #3.2
+atoms, 22 pseudobonds, 2 residues, 2 models selected
+> ui tool show "Selection Inspector"
+> style sel dashes 0
+Changed 2 pseudobond dashes
+> setattr sel g halfbond true
+Assigning halfbond attribute to 2 items
+> setattr sel g radius 0.155
+Assigning radius attribute to 2 items
+> select clear
+[Repeated 1 time(s)]
+> select add #3.2
+pseudobonds, 1 model selected
+> ui tool show "Selection Inspector"
+> style sel dashes 10
+Changed 1 pseudobond dash
+> setattr sel g radius 0.1
+Assigning radius attribute to 1 item
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_WIP.cxs"
+> select #3/B:319@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text "WAT 1"
+> select #3/B:348@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text "WAT 2"
+> style sel ball
+Changed 3 atom styles
+> select #3/B:319@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> style sel ball
+Changed 3 atom styles
+> select #3/B:201@MN
+atom, 1 residue, 1 model selected
+> label sel text Mn(II)
+> ui tool show "Color Actions"
+> color sel light gray target af
+> color sel light steel blue target af
+> color sel powder blue target af
+> color sel byelement target af
+> color sel #9071b8ff
+[Repeated 1 time(s)]
+> color sel #bd4794ff
+[Repeated 1 time(s)]
+> undo
+[Repeated 1 time(s)]
+> color sel #896baeff
+> color sel #44b582ff
+> color sel #8e6fb5ff
+[Repeated 1 time(s)]
+> color sel #8f70b7ff
+> color sel #9272baff
+> color sel #9575bfff
+> color sel #9e7ccaff
+> color sel #a07dccff
+> color sel #a17ecdff
+> color sel #a480d1ff
+> color sel #a984d7ff
+> color sel #ab85d9ff
+> color sel #ac86dbff
+> color sel #ad87dcff
+> color sel #af89dfff
+> color sel #b08ae1ff
+> color sel #b18be2ff
+> color sel #b28be3ff
+[Repeated 2 time(s)]
+> color sel #b38ce4ff
+> color sel #b48de6ff
+> color sel #b68ee8ff
+> color sel #bd93f0ff
+> color sel #bd94f1ff
+> color sel #be95f2ff
+> color sel #be95f3ff
+[Repeated 1 time(s)]
+> color sel #be95f2ff
+> color sel #be94f2ff
+> color sel #bd94f1ff
+> color sel #bd93f0ff
+> color sel #bc93f0ff
+[Repeated 3 time(s)]
+> color sel #bd94f1ff
+> color sel #be94f2ff
+> color sel #be95f2ff
+> color sel #bf95f4ff
+> color sel #c096f5ff
+[Repeated 1 time(s)]
+> color sel #c196f5ff
+> color sel #c197f6ff
+[Repeated 3 time(s)]
+> color sel #c096f5ff
+> color sel #c097f5ff
+> color sel #cdacf5ff
+> color sel #ceb0f5ff
+> color sel #d1b4f5ff
+> color sel #d1b5f5ff
+> color sel #d5bcf5ff
+> color sel #d6bdf5ff
+> color sel #d7c0f5ff
+> color sel #ddcaf5ff
+> color sel #e2d2f5ff
+> color sel #e7dcf5ff
+> color sel #e8ddf5ff
+> color sel #e9dff5ff
+[Repeated 2 time(s)]
+> color sel #e9def5ff
+> color sel #e8def5ff
+> color sel #e8ddf5ff
+[Repeated 1 time(s)]
+> color sel #e5d8f5ff
+> color sel #e4d6f5ff
+> color sel #e0d0f5ff
+> color sel #e0cff5ff
+> color sel #dfcdf5ff
+[Repeated 3 time(s)]
+> color sel #dfcef5ff
+> color sel #e1d1f5ff
+> color sel #e3d5f5ff
+> color sel #e6daf5ff
+> color sel #e7dbf5ff
+> color sel #e9e0f5ff
+> color sel #ebe2f5ff
+> color sel #ece5f5ff
+> color sel #eee8f5ff
+> color sel #f3f1f5ff
+> color sel #f4f2f5ff
+[Repeated 1 time(s)]
+> color sel #f3f2f5ff
+[Repeated 2 time(s)]
+> color sel #f4f2f5ff
+> color sel #f4f3f5ff
+> color sel #f5f5f5ff
+> color sel #f5f4f5ff
+> color sel #efebf5ff
+> color sel #eae2f5ff
+> color sel #e8def5ff
+> color sel #e6d9f5ff
+> color sel #e4d6f5ff
+> color sel #e3d5f5ff
+> color sel #e3d4f5ff
+[Repeated 1 time(s)]
+> color sel #e3d5f5ff
+[Repeated 1 time(s)]
+> color sel #e4d7f5ff
+> color sel #e6daf5ff
+> color sel #e8ddf5ff
+> color sel #e8def5ff
+[Repeated 3 time(s)]
+> color sel #e8ddf5ff
+[Repeated 2 time(s)]
+> color sel #e7dcf5ff
+> color sel #e7dbf5ff
+> color sel #e6dbf5ff
+> color sel #e6daf5ff
+> color sel #e5d8f5ff
+> color sel #e4d6f5ff
+[Repeated 1 time(s)]
+> color sel #e3d5f5ff
+[Repeated 1 time(s)]
+> color sel #e3d4f5ff
+[Repeated 1 time(s)]
+> color sel #e2d3f5ff
+> color sel #e1d1f5ff
+> color sel #e1d0f5ff
+> color sel #ddcaf5ff
+> color sel #dcc8f5ff
+> color sel #dbc6f5ff
+> color sel #d9c3f5ff
+[Repeated 1 time(s)]
+> color sel #d9c2f5ff
+> color sel #d8c1f5ff
+[Repeated 1 time(s)]
+> color sel #d8c0f5ff
+> color sel #d7c0f5ff
+[Repeated 1 time(s)]
+> color sel #d8c0f5ff
+> color sel #dac4f5ff
+> color sel #ddcaf5ff
+> color sel #dfcef5ff
+> color sel #e0d0f5ff
+> color sel #e1d0f5ff
+> color sel #e1d1f5ff
+> color sel #e2d2f5ff
+[Repeated 1 time(s)]
+> color sel #e2d3f5ff
+> color sel #e2d4f5ff
+> color sel #e3d4f5ff
+> color sel #e3d5f5ff
+[Repeated 1 time(s)]
+> color sel #e4d6f5ff
+> color sel #e5d7f5ff
+> color sel #e5d8f5ff
+> color sel #e5d8f6ff
+> color sel #eee0ffff
+[Repeated 1 time(s)]
+> color sel #e6d2ffff
+> color sel #e0c8ffff
+> color sel #d1acffff
+> color sel #cfa9ffff
+> color sel #cfaaffff
+> color sel #d0aaffff
+> color sel #d0abffff
+> color sel #d2aeffff
+> color sel #d5b3ffff
+> color sel #d7b8ffff
+> color sel #dabdffff
+> color sel #dbbeffff
+> color sel #ddc2ffff
+> color sel #dec4ffff
+> color sel #dfc6ffff
+> color sel #e0c8ffff
+> color sel #e1c8ffff
+> color sel #e1c9ffff
+> color sel #e2ccffff
+> color sel #e5d1ffff
+> color sel #e7d5ffff
+> color sel #e9d8ffff
+> color sel #eadaffff
+[Repeated 2 time(s)]
+> color sel #ead9ffff
+[Repeated 1 time(s)]
+> color sel #ead8ffff
+> color sel #e9d7ffff
+> color sel #e8d5ffff
+> color sel #e6d3ffff
+> color sel #e6d2ffff
+[Repeated 1 time(s)]
+> color sel #e6d1ffff
+> color sel #e4ceffff
+> color sel #e2caffff
+> color sel #e1c8ffff
+> color sel #e0c7ffff
+[Repeated 1 time(s)]
+> color sel #e0c6ffff
+> color sel #dfc6ffff
+[Repeated 2 time(s)]
+> color sel #dfc5ffff
+> color sel #dec5ffff
+> color sel #dcc0ffff
+> color sel #dbbfffff
+> color sel #d9bbffff
+> color sel #d9baffff
+> color sel #d8b8ffff
+> color sel #d7b8ffff
+[Repeated 1 time(s)]
+> color sel #d7b7ffff
+[Repeated 1 time(s)]
+> color sel #d7b8ffff
+> color sel #d8b9ffff
+> color sel #d9bbffff
+> color sel #dabdffff
+> color sel #dcc0ffff
+> color sel #ddc2ffff
+> color sel #dfc6ffff
+> color sel #e0c7ffff
+> color sel #e1caffff
+> color sel #e2cbffff
+> color sel #e2ccffff
+> color sel #e3ccffff
+[Repeated 1 time(s)]
+> color sel #e2cbffff
+> color sel #e1c9ffff
+> color sel #dfc6ffff
+> color sel #ddc3ffff
+> color sel #ddc2ffff
+> color sel #dcc0ffff
+> color sel #dbbeffff
+> color sel #dabdffff
+[Repeated 1 time(s)]
+> ui tool show "Color Actions"
+> color sel hot pink target af
+> color sel dark violet target af
+> color sel deep pink target af
+> color sel hot pink target af
+> show #!1 models
+> hide #!3 models
+> show #!3 models
+> hide #!1 models
+> color sel #ff69b4ff
+[Repeated 1 time(s)]
+> color sel #ff79bcff
+> color sel #ff9ecfff
+> color sel #ffa4d2ff
+> color sel #ffa8d3ff
+> color sel #ffb3d9ff
+> color sel #ffb4d9ff
+> color sel #ffb6daff
+> color sel #ffb7dbff
+> color sel #ffbedeff
+> color sel #ffc6e3ff
+> color sel #ffc9e4ff
+> color sel #ffcce5ff
+> color sel #ffcce6ff
+[Repeated 3 time(s)]
+> color sel #ffcce5ff
+> color sel #ffcbe5ff
+[Repeated 2 time(s)]
+> color sel #ffcce6ff
+> color sel #ffcde6ff
+> color sel #ffd0e7ff
+> color sel #ffd0e8ff
+> color sel #ffd6ebff
+> color sel #ffd8ecff
+> color sel #ffe3f1ff
+> color sel #ffe9f4ff
+> color sel #ffeaf4ff
+[Repeated 1 time(s)]
+> color sel #ffe9f4ff
+[Repeated 2 time(s)]
+> color sel #ffe8f4ff
+> color sel #ffe8f3ff
+> color sel #ffe7f3ff
+[Repeated 1 time(s)]
+> color sel #ffe6f3ff
+> color sel #ffe5f2ff
+> color sel #ffe2f1ff
+> color sel #ffe0efff
+> color sel #ffdcedff
+> color sel #ffdbedff
+> color sel #ffd9ecff
+[Repeated 3 time(s)]
+> color sel #ffdaecff
+> color sel #ffdcedff
+> color sel #ffddeeff
+> color sel #ffdeefff
+> color sel #ffe0f0ff
+> color sel #ffe1f0ff
+[Repeated 1 time(s)]
+> color sel #ffe2f0ff
+> color sel #ffe2f1ff
+> color sel #ffe3f1ff
+[Repeated 2 time(s)]
+> color sel #ffe4f1ff
+[Repeated 1 time(s)]
+> color sel #ffe4f2ff
+[Repeated 1 time(s)]
+> color sel #ffe2f1ff
+> color sel #ffe0f0ff
+> color sel #ffdbedff
+> color sel #ffd9ecff
+[Repeated 1 time(s)]
+> color sel #ffd8ecff
+> color sel #ffd6ebff
+> color sel #ffd4eaff
+> color sel #ffd4e9ff
+> color sel #ffd2e8ff
+> color sel #ffd0e7ff
+> color sel #ffcee7ff
+> color sel #ffcce6ff
+> color sel #ffcbe5ff
+[Repeated 3 time(s)]
+> color sel #ffcce5ff
+[Repeated 1 time(s)]
+> color sel #ffcbe5ff
+> color sel #ffc5e2ff
+> color sel #ffb6dbff
+> color sel #ffb6daff
+> color sel #ffb5daff
+[Repeated 3 time(s)]
+> color sel #ffb4d9ff
+> color sel #ffb3d9ff
+> color sel #ffb2d8ff
+> color sel #ffb1d8ff
+> color sel #ffaed6ff
+> color sel #ffadd6ff
+> color sel #ffacd6ff
+> color sel #ffacd5ff
+> color sel #ffacd6ff
+> color sel #ffadd6ff
+> color sel #ffaed6ff
+> color sel #ffaed7ff
+> color sel #ffafd7ff
+[Repeated 2 time(s)]
+> color sel #ffb0d7ff
+> color sel #ffb0d8ff
+> color sel #ffb1d8ff
+> color sel #ffb2d8ff
+[Repeated 1 time(s)]
+> color sel #ffb2d9ff
+> color sel #ffb3d9ff
+> color sel #ffbbddff
+> color sel #ffbcddff
+> color sel #ffbcdeff
+> color sel #ffbedeff
+> color sel #ffc1e0ff
+> color sel #ffcae4ff
+> color sel #ffcde6ff
+> color sel #ffcfe7ff
+[Repeated 3 time(s)]
+> color sel #ffcee7ff
+> color sel #ffcee6ff
+> color sel #ffcde6ff
+> color sel #ffcce5ff
+> color sel #ffcae5ff
+[Repeated 1 time(s)]
+> color sel #ffcbe5ff
+[Repeated 1 time(s)]
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_WIP.cxs"
+> show #!2 models
+> hide #!2 models
+> view active-site-2
+> select clear
+> hide #2.1.3 models
+> view active-site-2
+> view active-site-3
+> view active-site-1
+> view active-site
+> view active-site-3
+> view active-site-1
+> view active-site-3
+> view active-site
+[Repeated 1 time(s)]
+> view active-site-3
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> show #!2 models
+> select add #2
+atoms, 13046 bonds, 48 pseudobonds, 1046 residues, 10 models selected
+> select subtract #2
+Nothing selected
+> select add #2
+atoms, 13046 bonds, 48 pseudobonds, 1046 residues, 10 models selected
+> select subtract #2
+Nothing selected
+> show #2.1.3 models
+> show #2.2.2 models
+> view active-site-3
+> view active-site
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site
+> view active-site-1
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> view active-site-1
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> view active-site-1
+[Repeated 1 time(s)]
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> mcopy #1 toAtoms #3 settings c matchResidues false
+Must specify one source molecule, got 2
+> mcopy #1.1 toAtoms #3 settings c matchResidues false
+> hide #!3 models
+> show #!3 models
+> select #3/d
+atoms, 3272 bonds, 5 pseudobonds, 262 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel olive target af
+> color sel sea green target af
+> color sel medium sea green target af
+> color sel forest green target af
+> color sel medium sea green target af
+> color sel green target af
+> color sel olive target af
+> color (#!3 & sel) byhetero
+> select clear
+> show #!1 models
+> hide #!1 models
+> select #3/c,d
+atoms, 6523 bonds, 11 pseudobonds, 523 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel sea green target af
+> color sel medium sea green target af
+> color sel lime green target af
+> color sel spring green target af
+> color sel lawn green target af
+> color sel green target af
+> color sel olive drab target af
+> color sel olive target af
+> color sel olive drab target af
+> ui tool show "Color Actions"
+> color sel olive drab target acsf
+> color sel dark olive green target acsf
+> color sel dark slate gray target acsf
+> color sel dark olive green target acsf
+> color sel dark green target acsf
+> color sel dark olive green target acsf
+> color sel olive drab target acsf
+> color sel byhetero target acsf
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_WIP.cxs"
+> select clear
+> select #3/c,d
+atoms, 6523 bonds, 11 pseudobonds, 523 residues, 2 models selected
+> ui tool show "Color Actions"
+> color sel indigo target acsf
+> color sel dark slate blue target acsf
+> color sel deep sky blue target acsf
+> color sel cyan target acsf
+> color sel olive drab target acsf
+> color sel sea green target acsf
+> color sel dodger blue target acsf
+> color sel turquoise target acsf
+> color sel teal target acsf
+> color sel steel blue target acsf
+> color sel cadet blue target acsf
+> color sel steel blue target acsf
+> color sel medium spring green target acsf
+> color sel dark turquoise target acsf
+> color sel midnight blue target acsf
+> color sel pale violet red target acsf
+> color sel medium purple target acsf
+> color sel purple target acsf
+> color sel dark magenta target acsf
+> color sel dark orchid target acsf
+> color sel medium violet red target acsf
+> color sel medium orchid target acsf
+> color sel dark violet target acsf
+> color sel rebecca purple target acsf
+> color sel dark slate blue target acsf
+> color sel indigo target acsf
+> color sel navy target acsf
+> color sel dark violet target acsf
+> color sel rebecca purple target acsf
+> color sel dark violet target acsf
+> color sel blue violet target acsf
+> color sel dark violet target acsf
+> color sel blue violet target acsf
+> color sel purple target acsf
+> color sel blue violet target acsf
+> color sel byhetero target acsf
+> view active-site-1
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red-
+> final_label.tif" width 1318 height 1080 supersample 4
+> hide #3.3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red-
+> final_unlabel.tif" width 1318 height 1080 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_fin.cxs"
+——— End of log from Sun Apr 27 12:08:58 2025 ———
+> view name session-start
+opened ChimeraX session
+> delete sel
+> ~bond sel
+> select #3/B:319@O
+atom, 1 residue, 1 model selected
+> select add #3/B:201@MN
+atoms, 2 residues, 1 model selected
+> ~bond sel
+> delete bonds sel
+> select #3/B:201@MN
+atom, 1 residue, 1 model selected
+> select add #3/B:319@O
+atoms, 2 residues, 1 model selected
+> delete bonds sel
+> select clear
+> select #3/B:143@DG3
+atom, 1 residue, 1 model selected
+> select add #3/B:143@DB3
+atoms, 1 residue, 1 model selected
+> bond sel
+Created 0 bonds
+> select #3/B:143@DE22
+atom, 1 residue, 1 model selected
+> select add #3/B:34@OH
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 0 bonds
+> bond sel res f
+Expected a keyword
+> bond sel resonable false
+Expected a keyword
+> ui tool show "Selection Inspector"
+> select clear
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select clear
+> select #3/B:74@NE2
+atom, 1 residue, 1 model selected
+> select add #3/B:74@CE1
+atoms, 1 residue, 1 model selected
+> select #3/B:30@DB3
+atom, 1 residue, 1 model selected
+> select add #3/B:30@CB
+atoms, 1 residue, 1 model selected
+> select #3/B:348@O
+atom, 1 residue, 1 model selected
+> select add #3/B:348@D2
+atoms, 1 residue, 1 model selected
+> ~bond sel
+> bond sel
+Created 1 bond
+> select #3/B:30@DD1
+atom, 1 residue, 1 model selected
+> select add #3/B:30@DB3
+atoms, 1 residue, 1 model selected
+> pbond sel
+> ~pbond sel
+No pseudobond between combination #3/B HIS 30 DD1 and combination #3/B HIS 30
+DB3 found for custom #3.5
+> ui tool show "Selection Inspector"
+> setattr =sel p halfbond false
+Assigning halfbond attribute to 1 item
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 1 item
+> ui tool show "Selection Inspector"
+> setattr =sel p halfbond false
+Assigning halfbond attribute to 1 item
+> color sel byhetero target p
+> select #3/B:163@NE2
+atom, 1 residue, 1 model selected
+> select add #3/B:201@MN
+atoms, 2 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 1 item
+> color =sel byhetero target p
+> select #3/B:163@NE2
+atom, 1 residue, 1 model selected
+> select add #3/B:201@MN
+atoms, 2 residues, 1 model selected
+> color =sel byhetero target p halfbond false
+> color sel byhetero target p halfbond false
+> color sel byhetero target p halfbond true
+> color sel byhetero target p halfbond false
+> color sel byhetero target p
+> color sel byhetero target p halfbond true
+> select #3/B:161@CH2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/B:73@CB
+atom, 1 residue, 1 model selected
+> select up
+atoms, 13 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> hide #3.4 models
+> show #3.4 models
+> ui tool show "Selection Inspector"
+> setattr =sel p display false
+Assigning display attribute to 1 item
+> setattr =sel p display true
+Assigning display attribute to 1 item
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> ui tool show "Selection Inspector"
+> setattr =sel p display false
+Assigning display attribute to 1 item
+> help help:user
+> view name wat1-q143
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!2.2 models
+> show #!2.2 models
+> hide #!2.2 models
+> hide #2.2.2 models
+> hide #2.2.1 models
+> hide #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #3.5 models
+> show #3.5 models
+> hide #!1 models
+> hide #!3 models
+> show #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!3 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> select #1.1/B:161@CE2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #1.1/B:73@CB
+atom, 1 residue, 1 model selected
+> select #1.1/B:73@CB
+atom, 1 residue, 1 model selected
+> select up
+atoms, 13 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox_wat1-q143.tif"
+> width 935 height 859 supersample 4 transparentBackground true
+> show #!3 models
+> hide #!1 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red_wat1-q143.tif"
+> width 935 height 859 supersample 3
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red_wat1-q143.tif"
+> width 935 height 859 supersample 4 transparentBackground true
+> ui tool show "Selection Inspector"
+> setattr =sel p display false
+Assigning display attribute to 1 item
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red_y166-H30.tif"
+> width 935 height 859 supersample 4 transparentBackground true
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!1 models
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> select #1.2/D:166@OH
+atom, 1 residue, 1 model selected
+> select sel @< 5
+atoms, 136 bonds, 7 pseudobonds, 26 residues, 10 models selected
+> show sel & #!1.1-2 atoms
+> hide #!1.2 models
+> show #!1.2 models
+> select up
+atoms, 378 bonds, 7 pseudobonds, 26 residues, 10 models selected
+> show sel & #!1.1-2 atoms
+> undo
+[Repeated 4 time(s)]
+> select clear
+> select #1.2/D:166@OH
+atom, 1 residue, 1 model selected
+> select up
+atoms, 20 bonds, 1 residue, 1 model selected
+> select up
+atoms, 122 bonds, 6 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> undo
+[Repeated 2 time(s)]
+> hide #!1 models
+> show #!1 models
+> show #!3 models
+> hide #!3 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!3 models
+> hide #!1 models
+> view name y166-h30
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site_red, session-start, wat1-q143, y166-h30
+> hide #!1.1 models
+> show #!1.1 models
+> hide #!1.1 models
+> hide #!1 models
+> hide #!3 models
+> open 7kks
+Summary of feedback from opening 7kks fetched from pdb
+---
+warnings | Atom D1 is not in the residue template for MET /A:0
+Atom D is not in the residue template for LYS /A:1
+Atom D is not in the residue template for HIS /A:2
+Atom D is not in the residue template for SER /A:3
+Atom D is not in the residue template for LEU /A:4
+Atom DA is not in the residue template for PRO /A:5
+Atom D is not in the residue template for ASP /A:6
+Atom D is not in the residue template for LEU /A:7
+Atom DA is not in the residue template for PRO /A:8
+Too many hydrogens missing from residue template(s) to warn about
+kks title:
+Neutron structure of Oxidized Human MnSOD [more info...]
+Chain information for 7kks #4
+---
+Chain | Description | UniProt
+A B | Superoxide dismutase [Mn], mitochondrial | SODM_HUMAN 1-198
+Non-standard residues in 7kks #4
+---
+MN3 — manganese (III) ion
+kks mmCIF Assemblies
+---
+| author_defined_assembly
+> select #4:166
+atoms, 40 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> select #4:166
+atoms, 40 bonds, 2 residues, 1 model selected
+> select sel @< 5 & ~sel
+atoms, 1113 bonds, 166 residues, 6 models selected
+> show sel & #!4 atoms
+> select up
+atoms, 2534 bonds, 166 residues, 6 models selected
+> show sel & #!4 atoms
+> hide sel & #!4 atoms
+> select clear
+> select #4/B:327@O
+atom, 1 residue, 1 model selected
+> hide #!4 models
+> view y166-h30
+> show #!3 models
+> select #3/B:540@D
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3273 bonds, 262 residues, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select clear
+> select #4:his
+atoms, 343 bonds, 20 residues, 1 model selected
+> select #3:his
+atoms, 688 bonds, 40 residues, 1 model selected
+> select #3:D
+Nothing selected
+> select #3:D8U
+atoms, 8 residues, 1 model selected
+> select #1:D8U
+Nothing selected
+> select #2:D8U
+atoms, 8 residues, 2 models selected
+> select #4:D8U
+Nothing selected
+> select #4@D8U
+Nothing selected
+> select #4@D
+atoms, 373 residues, 1 model selected
+> select #2@D
+atoms, 752 residues, 2 models selected
+> select #2.1@D
+atoms, 376 residues, 1 model selected
+> select #3@D
+atoms, 752 residues, 1 model selected
+> select #3@D
+atoms, 752 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> undo
+[Repeated 5 time(s)]
+> show #!4 models
+> hide #3.5 models
+> hide #3.4 models
+> show #3.4 models
+> show #3.5 models
+> hide #!3 models
+> select #4@D
+atoms, 373 residues, 1 model selected
+> show sel atoms
+[Repeated 1 time(s)]
+> ui tool show "Selection Inspector"
+> select up
+atoms, 5914 bonds, 373 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr sel r ribbon_hide_backbone false
+Assigning ribbon_hide_backbone attribute to 373 items
+> select clear
+> select #4@D
+atoms, 373 residues, 1 model selected
+> select #4@D*
+atoms, 518 residues, 1 model selected
+> show sel atoms
+> select up
+atoms, 6556 bonds, 518 residues, 1 model selected
+> show sel atoms
+> show #4 atoms
+> select clear
+> select #4/A:306@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3272 bonds, 259 residues, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select clear
+> hide #!4 models
+> view name y166-h30
+> show #!1 models
+> view name y166-h30
+> show #!2 models
+> hide #!2 models
+> hide #!1 models
+> show #!3 models
+> show #!1.1 models
+> hide #!1.2 models
+> hide #!1 models
+> select #3/B:540@D
+atom, 1 residue, 1 model selected
+> view sel
+> view name y166-h30
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini
+> review/MnSOD_Red_y166-H30_2.tif" width 935 height 859 supersample 4
+> transparentBackground true
+> show #!1 models
+> hide #!3 models
+> show #!3 models
+> hide #!1 models
+> hide #1.3 models
+> show #1.3 models
+> show #!1.2 models
+> hide #!3 models
+> hide #1.2.2 models
+> show #1.2:166 atoms
+> select #1.1/A:30
+atoms, 17 bonds, 1 residue, 1 model selected
+> show sel atoms
+> view y166-h30
+> select #1.1/A:22
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #1.1/A:30@DD1
+atom, 1 residue, 1 model selected
+> select sel @< 5
+atoms, 133 bonds, 1 pseudobond, 44 residues, 7 models selected
+> select sel & solvent
+atoms, 20 bonds, 13 residues, 6 models selected
+> show sel & #!1.1-2 atoms
+> select #1.1/A:306@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3272 bonds, 259 residues, 1 model selected
+> select #1.1/A:306@O
+atom, 1 residue, 1 model selected
+> show #!4 models
+> hide #!1 models
+> select add #1
+atoms, 13112 bonds, 31 pseudobonds, 1050 residues, 8 models selected
+> select subtract #1
+Nothing selected
+> select add #4
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 2 models selected
+> ui tool show "Selection Inspector"
+> setattr sel r ribbon_hide_backbone true
+Assigning ribbon_hide_backbone attribute to 525 items
+> setattr sel r ribbon_hide_backbone false
+Assigning ribbon_hide_backbone attribute to 525 items
+> setattr sel r ribbon_hide_backbone true
+Assigning ribbon_hide_backbone attribute to 525 items
+> select clear
+> select #4 and solvent
+Expected a keyword
+> select #4 & solvent
+atoms, 238 bonds, 125 residues, 1 model selected
+> select #4
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 2 models selected
+> show sel atoms
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!1 models
+> show #!1 models
+> hide #!4 models
+> select #1.1/B:30@ND1
+atom, 1 residue, 1 model selected
+> select sel @< 5
+atoms, 130 bonds, 10 pseudobonds, 39 residues, 12 models selected
+> select clear
+> select #1.1/B:30@ND1
+atom, 1 residue, 1 model selected
+> select sel :< 5 & solvent
+atoms, 21 bonds, 12 residues, 5 models selected
+> show sel & #!1.1-2 atoms
+> select #1.1/B:358@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 2 models selected
+> select up
+atoms, 4 bonds, 2 residues, 2 models selected
+> hide sel cartoons
+> hide sel atoms
+> select #1.1/B:347@O
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> style sel ball
+Changed 3 atom styles
+> select clear
+> select #1.2/D:166@OH
+atom, 1 residue, 1 model selected
+> hide #!1 models
+> show #!4 models
+> select #4/b:166
+atoms, 20 bonds, 1 residue, 1 model selected
+> view sel
+> ui tool show "Add Hydrogens"
+> addh #!4
+Summary of feedback from adding hydrogens to 7kks #4
+---
+notes | Termini for 7kks (#4) chain A determined from SEQRES records
+Termini for 7kks (#4) chain B determined from SEQRES records
+Chain-initial residues that are actual N termini: 7kks #4/A MET 0, 7kks #4/B
+MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: 7kks #4/A LYS 198, 7kks #4/B
+LYS 198
+Chain-final residues that are not actual C termini:
+hydrogen bonds
+hydrogens added
+> select clear
+> hide #!4 models
+> show #!1 models
+> hide #!1 models
+> show #!4 models
+> hide #!4 models
+> show #!1 models
+> addh #1.2
+Summary of feedback from adding hydrogens to 7kks #1.2
+---
+notes | Termini for 7kks (#1.2) chain A determined from SEQRES records
+Termini for 7kks (#1.2) chain D determined from SEQRES records
+Chain-initial residues that are actual N termini: 7kks #1.2/A MET 0, 7kks
+#1.2/D MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: 7kks #1.2/A LYS 198, 7kks
+#1.2/D LYS 198
+Chain-final residues that are not actual C termini:
+hydrogen bonds
+hydrogens added
+> show #!1 models
+> select #1.2/D:166@HH
+atom, 1 residue, 1 model selected
+> select #1.2@H*
+atoms, 23 residues, 1 model selected
+> delete sel
+> combine #1.1 #1.2
+Remapping chain ID 'A' in 7kks #1.2 to 'C'
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #5.2 models
+> show #5.2 models
+> hide #5.2 models
+> show #5.2 models
+> addh #5
+Summary of feedback from adding hydrogens to combination #5
+---
+notes | Termini for combination (#5) chain A determined from SEQRES records
+Termini for combination (#5) chain B determined from SEQRES records
+Termini for combination (#5) chain C determined from SEQRES records
+Termini for combination (#5) chain D determined from SEQRES records
+Chain-initial residues that are actual N termini: combination #5/A MET 0,
+combination #5/B MET 0, combination #5/C MET 0, combination #5/D MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: combination #5/A LYS 198,
+combination #5/B LYS 198, combination #5/C LYS 198, combination #5/D LYS 198
+Chain-final residues that are not actual C termini:
+hydrogen bonds
+hydrogens added
+> delete #5@H*
+> ui mousemode right pivot
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> ui mousemode right translate
+> ui mousemode right pivot
+> select #5/D:166@CG
+atom, 1 residue, 1 model selected
+> ui mousemode right "translate selected atoms"
+> undo
+> ui mousemode right pivot
+> hide #5.1 models
+> show #5.1 models
+> ui tool show H-Bonds
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@NE2
+atoms, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 restrict both interModel false twoColors
+> true intraRes false select true reveal true retainCurrent true
+hydrogen bonds found
+strict hydrogen bonds found
+> addh #5
+Summary of feedback from adding hydrogens to combination #5
+---
+notes | Termini for combination (#5) chain A determined from SEQRES records
+Termini for combination (#5) chain B determined from SEQRES records
+Termini for combination (#5) chain C determined from SEQRES records
+Termini for combination (#5) chain D determined from SEQRES records
+Chain-initial residues that are actual N termini: combination #5/A MET 0,
+combination #5/B MET 0, combination #5/C MET 0, combination #5/D MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: combination #5/A LYS 198,
+combination #5/B LYS 198, combination #5/C LYS 198, combination #5/D LYS 198
+Chain-final residues that are not actual C termini:
+hydrogen bonds
+hydrogens added
+> select #5/D:166@HH
+atom, 1 residue, 1 model selected
+> delete sel
+> ui mousemode right distance
+> distance #5/D:166@OH #5/B:30@HE2
+Distance between combination #5/D TYR 166 OH and /B HIS 30 HE2: 1.772Å
+> distance #5/B:30@HE2 #5/B:30@NE2
+Distance between combination #5/B HIS 30 HE2 and NE2: 1.010Å
+> ui mousemode right "translate selected atoms"
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> addh #5
+Summary of feedback from adding hydrogens to combination #5
+---
+notes | Termini for combination (#5) chain A determined from SEQRES records
+Termini for combination (#5) chain B determined from SEQRES records
+Termini for combination (#5) chain C determined from SEQRES records
+Termini for combination (#5) chain D determined from SEQRES records
+Chain-initial residues that are actual N termini: combination #5/A MET 0,
+combination #5/B MET 0, combination #5/C MET 0, combination #5/D MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: combination #5/A LYS 198,
+combination #5/B LYS 198, combination #5/C LYS 198, combination #5/D LYS 198
+Chain-final residues that are not actual C termini:
+hydrogen bonds
+hydrogens added
+> select #5/D:166@HH
+atom, 1 residue, 1 model selected
+> select up
+atoms, 21 bonds, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> delete sel
+> close #6
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> select #5/B:30@NE2
+atom, 1 residue, 1 model selected
+> select add #5/B:30@HE2
+atoms, 1 residue, 1 model selected
+> ~bond sel
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@HE2
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@NE2
+atoms, 2 residues, 1 model selected
+> ~pbond sel
+Cannot find pseudobond group named 'custom' for structure combination #5
+> delete sel pbond
+Expected a keyword
+> delete pbonds sel
+> select #5/B:30@NE2
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 1 pseudobond, 2 residues, 2 models selected
+> delete pbonds sel
+> select clear
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> select add #5/B:30@NE2
+atoms, 1 residue, 1 model selected
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> undo
+[Repeated 2 time(s)]
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@NE2
+atoms, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 restrict both interModel false twoColors
+> true intraRes false select true reveal true retainCurrent true
+hydrogen bonds found
+strict hydrogen bonds found
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel
+> ui mousemode right distance
+> distance #5/D:166@OH #5/B:30@HE2
+Distance between combination #5/D TYR 166 OH and /B HIS 30 HE2: 1.100Å
+> distance #5/B:30@HE2 #5/B:30@NE2
+Distance between combination #5/B HIS 30 HE2 and NE2: 1.700Å
+> show #!2 models
+> hide #!6 models
+> hide #!5 models
+> show #!5 models
+> hide #!2 models
+> hide #!5 models
+> show #!5 models
+> show #!3 models
+> show #!6 models
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> ui mousemode right "translate selected atoms"
+> ui tool show Angles/Torsions
+> hide #!6 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> close #4
+> show #!6 models
+> hide #!6 models
+> show #!3 models
+> hide #!5 models
+> select #3/D:166@CZ
+atom, 1 residue, 1 model selected
+> select add #3/D:166@OH
+atoms, 1 residue, 1 model selected
+> select add #3/B:540@D
+atoms, 2 residues, 1 model selected
+> show #!5 models
+> select #5/D:166@CZ
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 1 residue, 1 model selected
+> select add #5/B:30@HE2
+atoms, 2 residues, 1 model selected
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> show #!6 models
+> hide #!3 models
+> hide #!6 models
+> ui tool show "Selection Inspector"
+> setattr =sel p display false
+Assigning display attribute to 1 item
+> show #!6 models
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> select #5/D:166@CD1
+atom, 1 residue, 1 model selected
+> select #5/D:166@CD1
+atom, 1 residue, 1 model selected
+> select #5/D:166@CD1
+atom, 1 residue, 1 model selected
+> ui mousemode right pivot
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> ui mousemode right "translate selected atoms"
+> select clear
+> hide #5.3 models
+> show #5.3 models
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@NE2
+atoms, 2 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> select up
+atoms, 37 bonds, 2 residues, 1 model selected
+> select add #5
+atoms, 13167 bonds, 24 pseudobonds, 1050 residues, 5 models selected
+> ui tool show "Selection Inspector"
+> setattr =sel p display true
+Assigning display attribute to 24 items
+> hide #!6 models
+> hide #5.3 models
+> view y166-h30
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> select clear
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #5.3 models
+> hide #5.3 models
+> hide #!5 models
+> show #!5 models
+> select #5/B:336@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> select clear
+> show #!6 models
+> hide #!6 models
+> show #!6 models
+> hide #!6 models
+> view name y166-h30
+> ui mousemode right pivot
+> addh #5
+Summary of feedback from adding hydrogens to combination #5
+---
+warning | Not adding hydrogens to combination #5/B HIS 30 HE2 because it is missing heavy-atom bond partners
+notes | Termini for combination (#5) chain A determined from SEQRES records
+Termini for combination (#5) chain B determined from SEQRES records
+Termini for combination (#5) chain C determined from SEQRES records
+Termini for combination (#5) chain D determined from SEQRES records
+Chain-initial residues that are actual N termini: combination #5/A MET 0,
+combination #5/B MET 0, combination #5/C MET 0, combination #5/D MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: combination #5/A LYS 198,
+combination #5/B LYS 198, combination #5/C LYS 198, combination #5/D LYS 198
+Chain-final residues that are not actual C termini:
+hydrogen bonds
+hydrogens added
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 2 residues, 1 model selected
+> select #5/B:30@HN
+atom, 1 residue, 1 model selected
+> delete sel
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@HE2
+atoms, 2 residues, 1 model selected
+> ~bond sel
+> addh #5 hbond false
+Summary of feedback from adding hydrogens to combination #5
+---
+warning | Not adding hydrogens to combination #5/B HIS 30 HE2 because it is missing heavy-atom bond partners
+notes | Termini for combination (#5) chain A determined from SEQRES records
+Termini for combination (#5) chain B determined from SEQRES records
+Termini for combination (#5) chain C determined from SEQRES records
+Termini for combination (#5) chain D determined from SEQRES records
+Chain-initial residues that are actual N termini: combination #5/A MET 0,
+combination #5/B MET 0, combination #5/C MET 0, combination #5/D MET 0
+Chain-initial residues that are not actual N termini:
+Chain-final residues that are actual C termini: combination #5/A LYS 198,
+combination #5/B LYS 198, combination #5/C LYS 198, combination #5/D LYS 198
+Chain-final residues that are not actual C termini:
+hydrogens added
+> select #5/D:166@CZ
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 1 residue, 1 model selected
+> select add #5/D:166@HH
+atoms, 1 residue, 1 model selected
+> select #5/B:30@HE21
+atom, 1 residue, 1 model selected
+> delete sel
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> show #!6 models
+> select #5/D:166@HH
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 1 residue, 1 model selected
+> ui mousemode right distance
+> distance #5/D:166@HH #5/D:166@OH
+Distance between combination #5/D TYR 166 HH and OH: 0.960Å
+> select clear
+> ui tool show "Selection Inspector"
+[Repeated 1 time(s)]
+> select clear
+> ui tool show "Selection Inspector"
+> select #5/D:166@HH
+atom, 1 residue, 1 model selected
+> select add #5/D:166@OH
+atoms, 1 residue, 1 model selected
+> ui tool show "Selection Inspector"
+Drag select of 2 atoms, 3 bonds, 2 pseudobonds
+> ui tool show "Selection Inspector"
+> setattr =sel p display false
+Assigning display attribute to 2 items
+> setattr =sel p display true
+Assigning display attribute to 2 items
+Drag select of 1 atoms, 1 bonds, 1 pseudobonds
+> ui tool show "Selection Inspector"
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/D:166@HH
+atoms, 1 residue, 1 model selected
+> ~pbond sel
+No pseudobond between combination #5/D TYR 166 OH and combination #5/D TYR 166
+HH found for custom #5.3
+Drag select of 1 atoms, 1 bonds, 1 pseudobonds
+> select subtract #5/D:166@OH
+Nothing selected
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+Drag select of 1 atoms, 1 bonds, 1 pseudobonds
+> delete pbonds sel
+> select clear
+> view y166-h30
+> ui mousemode right "translate selected atoms"
+> select #5/B:30@HE2
+atom, 1 residue, 1 model selected
+> show #!3 models
+> hide #!3 models
+> view y166-h30
+> hide #!6 models
+> select clear
+> select #5/D:166@HH
+atom, 1 residue, 1 model selected
+> delete sel
+> view y166-h30
+> show #!6 models
+> hide #!6 models
+> select #5/D:166@CE1
+atom, 1 residue, 1 model selected
+> select clear
+> select #5/d
+atoms, 3298 bonds, 5 pseudobonds, 266 residues, 2 models selected
+> lighting flat
+> color (#!5 & sel) #9dfedeff
+[Repeated 2 time(s)]
+> color (#!5 & sel) #9dfee0ff
+> color (#!5 & sel) #9dfee1ff
+> color (#!5 & sel) #9dfee3ff
+> color (#!5 & sel) #9dfee6ff
+> color (#!5 & sel) #9dfee8ff
+> color (#!5 & sel) #9dfeeaff
+> color (#!5 & sel) #9dfeecff
+> color (#!5 & sel) #9dfeeeff
+> color (#!5 & sel) #9dfeefff
+> color (#!5 & sel) #9dfef0ff
+> color (#!5 & sel) #9dfef1ff
+> color (#!5 & sel) #9dfef2ff
+> color (#!5 & sel) #9dfef3ff
+> color (#!5 & sel) #9dfef4ff
+> color (#!5 & sel) #9dfef5ff
+> color (#!5 & sel) #9dfef7ff
+> color (#!5 & sel) #9dfef8ff
+> color (#!5 & sel) #9dfef9ff
+> color (#!5 & sel) #9dfefaff
+> color (#!5 & sel) #9dfefbff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9dfefaff
+> color (#!5 & sel) #9dfef9ff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9dfef6ff
+> color (#!5 & sel) #9dfef4ff
+> color (#!5 & sel) #9dfef1ff
+> color (#!5 & sel) #9dfeefff
+> color (#!5 & sel) #9dfeeeff
+> color (#!5 & sel) #9dfeecff
+> color (#!5 & sel) #9dfeebff
+> color (#!5 & sel) #9dfeeaff
+> color (#!5 & sel) #9dfee9ff
+> color (#!5 & sel) #9dfee8ff
+> color (#!5 & sel) #9dfee6ff
+> color (#!5 & sel) #9dfee4ff
+> color (#!5 & sel) #9dfee1ff
+> color (#!5 & sel) #9dfedeff
+> color (#!5 & sel) #9dfed6ff
+> color (#!5 & sel) #9dfecbff
+> color (#!5 & sel) #9dfec6ff
+> color (#!5 & sel) #9dfec4ff
+> color (#!5 & sel) #9dfec0ff
+> color (#!5 & sel) #9dfeb5ff
+> color (#!5 & sel) #9dfea3ff
+> color (#!5 & sel) #9dfe93ff
+> color (#!5 & sel) #9dfe8aff
+> color (#!5 & sel) #9dfe85ff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9dfe87ff
+> color (#!5 & sel) #9dfe8fff
+> color (#!5 & sel) #9dfe98ff
+> color (#!5 & sel) #9dfea7ff
+> color (#!5 & sel) #9dfeb4ff
+> color (#!5 & sel) #9dfec0ff
+> color (#!5 & sel) #9dfec8ff
+> color (#!5 & sel) #9dfed0ff
+> color (#!5 & sel) #9dfee6ff
+> color (#!5 & sel) #9dfef4ff
+> color (#!5 & sel) #9dfeffff
+> color (#!5 & sel) #9dfefeff
+> color (#!5 & sel) #9dfef9ff
+> color (#!5 & sel) #9dfef2ff
+> color (#!5 & sel) #9dfef0ff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9df6f0ff
+> color (#!5 & sel) #9deaf0ff
+> color (#!5 & sel) #9de4f0ff
+> color (#!5 & sel) #9de1f0ff
+> color (#!5 & sel) #9ddff0ff
+> color (#!5 & sel) #9ddcf0ff
+> color (#!5 & sel) #9ddbf0ff
+> color (#!5 & sel) #9ddaf0ff
+> color (#!5 & sel) #9dd8f0ff
+> color (#!5 & sel) #9dd5f0ff
+> color (#!5 & sel) #9dd1f0ff
+> color (#!5 & sel) #9dcff0ff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9dcef0ff
+> color (#!5 & sel) #9dc5f0ff
+> color (#!5 & sel) #9db9f0ff
+> color (#!5 & sel) #9db3f0ff
+> color (#!5 & sel) #9db0f0ff
+> color (#!5 & sel) #9daff0ff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9db0f0ff
+> color (#!5 & sel) #9db1f0ff
+> color (#!5 & sel) #9db4f0ff
+> color (#!5 & sel) #9db7f0ff
+> color (#!5 & sel) #9dbdf0ff
+> color (#!5 & sel) #9dc8f0ff
+> color (#!5 & sel) #9dcdf0ff
+> color (#!5 & sel) #9dcef0ff
+> color (#!5 & sel) #9dcff0ff
+[Repeated 2 time(s)]
+> color (#!5 & sel) #9dd0f0ff
+> color (#!5 & sel) #9dd2f0ff
+> color (#!5 & sel) #9dd4f0ff
+> color (#!5 & sel) #9dd6f0ff
+> color (#!5 & sel) #9dd8f0ff
+> color (#!5 & sel) #9dd9f0ff
+> color (#!5 & sel) #9ddaf0ff
+> color (#!5 & sel) #9ddcf0ff
+> color (#!5 & sel) #9dddf0ff
+> color (#!5 & sel) #9ddef0ff
+> color (#!5 & sel) #9ddff0ff
+[Repeated 1 time(s)]
+> color (#!5 & sel) #9ddef0ff
+> color (#!5 & sel) #9ddcf0ff
+> color (#!5 & sel) #9dd7f0ff
+> color (#!5 & sel) #9dd6f0ff
+> color (#!5 & sel) #9dd4f0ff
+> color (#!5 & sel) #9dd3f0ff
+> color (#!5 & sel) #9dd1f0ff
+> color (#!5 & sel) #9dd0f0ff
+[Repeated 1 time(s)]
+> lighting full
+> lighting simple
+> lighting full
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting flat
+[Repeated 1 time(s)]
+> lighting full
+> lighting soft
+> lighting full
+> lighting flat
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> lighting full
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> hide #!5 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> show #!2 models
+> hide #!2 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2.2 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!3 models
+> show #!5 models
+> color (#!5 & sel) #9dd0e3ff
+> color (#!5 & sel) #9dd0d3ff
+> color (#!5 & sel) #9dd0a1ff
+> color (#!5 & sel) #9dd093ff
+> color (#!5 & sel) #9dd092ff
+> color (#!5 & sel) #9dd09aff
+> color (#!5 & sel) #9dd0a4ff
+> color (#!5 & sel) #9dd0ccff
+> color (#!5 & sel) #9dd0d7ff
+> color (#!5 & sel) #9dd0ddff
+> color (#!5 & sel) #9dd0e1ff
+> color (#!5 & sel) #9dd0ecff
+> color (#!5 & sel) #9dd0f7ff
+> color (#!5 & sel) #9dd0f8ff
+> color (#!5 & sel) #9dd0feff
+> color (#!5 & sel) #9dd0ffff
+[Repeated 1 time(s)]
+> hide #!5 models
+> lighting flat
+> color #3.1-2,4-5#!3 #a032ffff
+> undo
+> show #!5 models
+> color (#!5 & sel) #a032ffff
+> color (#!5 & sel) byhetero
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!2.2 models
+> show #!2.2 models
+> hide #!2.2 models
+> hide #!2 models
+> hide #!3 models
+> lighting full
+> lighting shadows false
+> lighting shadows true
+> select clear
+> view name y166-h30
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox_y166-H30.tif"
+> width 1075 height 859 supersample 4
+> show #!3 models
+> hide #!5 models
+> hide #!3 models
+> show #!3 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> lighting shadows false
+> select #3/B:30@ND1
+atom, 1 residue, 1 model selected
+> select sel :<5 & solvent
+atoms, 29 bonds, 15 residues, 5 models selected
+> show sel & #!3 atoms
+> select #3/D:335@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!5 models
+> hide #!5 models
+> show #!2 models
+> hide #!2 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> select #3/B:352@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view y166-h30
+> select #3/D:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view y166-h30
+[Repeated 1 time(s)]
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red_y166-H30.tif"
+> width 1075 height 859 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD.tif" width 1075
+> height 859 supersample 3
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_fin.cxs"
+——— End of log from Fri Aug 15 23:42:37 2025 ———
+> view name session-start
+opened ChimeraX session
+> show #!6 models
+> ui mousemode right distance
+> distance #3/B:30@DD1 #3/B:348@O
+Distance between combination #3/B HIS 30 DD1 and DOD 348 O: 2.922Å
+> hide #!3 models
+> show #!5 models
+> close #6
+> show #!3 models
+> hide #!3 models
+> ui tool show "Selection Inspector"
+> style sel dashes 0
+Changed 1 pseudobond dash
+> setattr sel g halfbond true
+Assigning halfbond attribute to 1 item
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> ui tool show "Selection Inspector"
+> hide #!3 models
+> select clear
+> ui tool show "Selection Inspector"
+> ui mousemode right "translate selected atoms"
+> ui mousemode right pivot
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> cofr frontCenter
+> select #5/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:336@D1
+atoms, 2 residues, 1 model selected
+> select add #5/B:336@O
+atoms, 2 residues, 1 model selected
+> select add #5/B:347@D2
+atoms, 3 residues, 1 model selected
+> select add #5/B:347@D1
+atoms, 3 residues, 1 model selected
+> select add #5/B:30@ND1
+atoms, 4 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 restrict both interModel false distSlop
+> 0.5 intraRes false select true reveal true retainCurrent true
+hydrogen bonds found
+> select add #5/B:336@O
+atoms, 2 residues, 1 model selected
+> select add #5/B:347@D2
+atoms, 3 residues, 1 model selected
+> select add #5/B:347@D1
+atoms, 3 residues, 1 model selected
+> select add #5/B:30@ND1
+atoms, 4 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 restrict both interModel false distSlop
+> 0.7 intraRes false reveal true retainCurrent true
+hydrogen bonds found
+> help help:user/tools/hbonds.html
+> hbonds sel color #00fdff dashes 6 restrict both interModel false distSlop
+> 1.0 intraRes false reveal true retainCurrent true
+hydrogen bonds found
+> select clear
+> select #5/B:336@O
+atom, 1 residue, 1 model selected
+> select add #5/B:347@D2
+atoms, 2 residues, 1 model selected
+> pbond sel
+> show #5.3 models
+> select clear
+> delete pbonds sel
+> select #5/B:30@ND1
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> distance #5/B:30@ND1 #5/B:347@D1
+Distance between combination #5/B HIS 30 ND1 and HOH 347 D1: 2.690Å
+> distance #5/B:30@ND1 #5/B:347@D2
+Distance between combination #5/B HIS 30 ND1 and HOH 347 D2: 2.751Å
+> hide #!4 models
+> select #5/B:347@D1
+atom, 1 residue, 1 model selected
+> select add #5/B:30@ND1
+atoms, 2 residues, 1 model selected
+> pbond sel
+> select up
+pseudobonds, 1 model selected
+> ui tool show "Color Actions"
+> color sel cyan target p
+> select clear
+> color sel deep sky blue target p
+> select clear
+> color sel cyan target p
+> select clear
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site_red, session-start, wat1-q143, y166-h30
+> view active-site
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site_red
+> view active-site
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> select #5/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #5/B:161@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #5 & @@ display
+atoms, 583 bonds, 26 pseudobonds, 53 residues, 5 models selected
+> select #5/b & @@ display
+atoms, 158 bonds, 11 pseudobonds, 13 residues, 5 models selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 restrict both interModel false distSlop
+> 0.5 intraRes false reveal true retainCurrent true
+hydrogen bonds found
+> select clear
+> select #5/B:327@O
+atom, 1 residue, 1 model selected
+> select add #5/B:143@DE21
+atoms, 2 residues, 1 model selected
+> pbond sel
+> ui tool show "Selection Inspector"
+> color sel cyan target p
+> select clear
+[Repeated 2 time(s)]
+> delete pbonds sel
+> select clear
+> select #5/B:161@DA
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #5/b & @@ display
+atoms, 157 bonds, 14 pseudobonds, 13 residues, 5 models selected
+> select #5/b & @@ display & ~backbone
+atoms, 117 bonds, 13 pseudobonds, 13 residues, 5 models selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 interModel false distSlop 0.5 intraRes
+> false reveal true retainCurrent true
+hydrogen bonds found
+> select #5/B:346@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> delete pbonds sel
+> select clear
+> view active-site
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site_red
+> ui mousemode right select
+> select clear
+[Repeated 1 time(s)]
+> lighting full
+[Repeated 1 time(s)]
+> lighting shadows false
+> lighting soft
+> lighting simple
+> lighting full
+> lighting shadows false
+> view name active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site_red
+> view active-site
+> view active-site-1
+> select clear
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!1 models
+> select #5/B:34@HH
+atom, 1 residue, 1 model selected
+> select add #5/B:327@H1
+atoms, 2 residues, 1 model selected
+> delete atoms sel
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site_red, session-start, wat1-q143, y166-h30
+> view active-site_red
+> help help:user
+> select #5 & main & @D
+atoms, 746 residues, 1 model selected
+> select #5 & main & @O
+atoms, 796 residues, 1 model selected
+> select #5 & main & D
+atoms, 2 residues, 1 model selected
+> select #5/B:163@DD1
+atom, 1 residue, 1 model selected
+> select #5 & main & @D*
+atoms, 796 residues, 1 model selected
+> select add #5/B:30@HE2
+atoms, 796 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> size sel atomRadius 0.99
+Changed 6129 atom radii
+> size sel atomRadius 0.98
+Changed 6129 atom radii
+> size sel atomRadius 0.97
+Changed 6129 atom radii
+> size sel atomRadius 0.96
+Changed 6129 atom radii
+> size sel atomRadius 0.95
+Changed 6129 atom radii
+> size sel atomRadius 0.94
+Changed 6129 atom radii
+> size sel atomRadius 0.93
+Changed 6129 atom radii
+> size sel atomRadius 0.92
+Changed 6129 atom radii
+> size sel atomRadius 0.91
+Changed 6129 atom radii
+> size sel atomRadius 0.9
+Changed 6129 atom radii
+> size sel atomRadius 0.89
+Changed 6129 atom radii
+> size sel atomRadius 0.88
+Changed 6129 atom radii
+> size sel atomRadius 0.87
+Changed 6129 atom radii
+> size sel atomRadius 0.86
+Changed 6129 atom radii
+> size sel atomRadius 0.85
+Changed 6129 atom radii
+> size sel atomRadius 0.84
+Changed 6129 atom radii
+> size sel atomRadius 0.83
+Changed 6129 atom radii
+> size sel atomRadius 0.82
+Changed 6129 atom radii
+> size sel atomRadius 0.81
+Changed 6129 atom radii
+> size sel atomRadius 0.8
+Changed 6129 atom radii
+> size sel atomRadius 0.79
+Changed 6129 atom radii
+> size sel atomRadius 0.78
+Changed 6129 atom radii
+> size sel atomRadius 0.77
+Changed 6129 atom radii
+> size sel atomRadius 0.5
+Changed 6129 atom radii
+> style sel ball
+Changed 6129 atom styles
+> style sel stick
+Changed 6129 atom styles
+> size sel atomRadius 1.2
+Changed 6129 atom radii
+> size sel atomRadius 0.8
+Changed 6129 atom radii
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> hide sel atoms
+> show sel atoms
+> undo
+[Repeated 10 time(s)]No undo action is available
+> undo
+No undo action is available
+> undo
+No undo action is available
+> undo
+No undo action is available
+> undo
+No undo action is available
+> undo
+No undo action is available
+> undo
+No undo action is available
+> undo
+No undo action is available
+> select #5 & main & @D* & @@display
+atoms, 41 residues, 1 model selected
+> select #5 & main & @D* & @@display & ~/a
+atoms, 30 residues, 1 model selected
+> select #5/~a & main & @D* & @@display &
+Expected an objects specifier or a keyword
+> select #5/b,d & main & @D* & @@display &
+Expected a keyword
+> select #5/b,d & main & @D* & @@display
+atoms, 23 residues, 1 model selected
+> select up
+atoms, 389 bonds, 23 residues, 1 model selected
+> select down
+atoms, 23 residues, 1 model selected
+> select add #5/B:30@HE2
+atoms, 23 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> size sel atomRadius 1
+Changed 134 atom radii
+> size sel stickRadius -0.0.5
+Invalid "stickRadius" argument: Expected a number >= 0 or a +/- delta
+> size sel stickRadius -0.05
+Changed 0 bond radii
+> size sel stickRadius 0.1
+Changed 0 bond radii
+> select up
+atoms, 1 bond, 23 residues, 1 model selected
+> select down
+atoms, 1 bond, 23 residues, 1 model selected
+> select up
+atoms, 1 bond, 23 residues, 1 model selected
+> select down
+atoms, 1 bond, 23 residues, 1 model selected
+> select up
+atoms, 1 bond, 23 residues, 1 model selected
+> select down
+atoms, 1 bond, 23 residues, 1 model selected
+> select up
+atoms, 1 bond, 23 residues, 1 model selected
+> select up
+atoms, 389 bonds, 23 residues, 1 model selected
+> select down
+atoms, 1 bond, 23 residues, 1 model selected
+> select down
+atoms, 1 bond, 23 residues, 1 model selected
+> select up
+atoms, 389 bonds, 23 residues, 1 model selected
+> select down
+atoms, 23 residues, 1 model selected
+> select add #5/B:34@CD1
+atoms, 23 residues, 1 model selected
+> select up
+atoms, 389 bonds, 23 residues, 1 model selected
+> select down
+atoms, 23 residues, 1 model selected
+> select subtract #5/B:34@CD1
+atoms, 23 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> style sel ball
+Changed 134 atom styles
+> style sel stick
+Changed 134 atom styles
+> select clear
+[Repeated 1 time(s)]
+> select add #5/B:163@DD2
+atom, 1 bond, 1 residue, 1 model selected
+> select subtract #5/B:163@DD2
+bond, 1 model selected
+> select add #5/B:163@DD2
+atom, 1 bond, 1 residue, 1 model selected
+> select subtract #5/B:163@DD2
+bond, 1 model selected
+> select up
+atoms, 4 bonds, 1 residue, 1 model selected
+> select down
+bonds, 1 model selected
+> ui tool show "Selection Inspector"
+> size =sel stickRadius 0.19
+Changed 3 bond radii
+> size =sel stickRadius 0.18
+Changed 3 bond radii
+> size =sel stickRadius 0.17
+Changed 3 bond radii
+> size =sel stickRadius 0.16
+Changed 3 bond radii
+> size =sel stickRadius 0.15
+Changed 3 bond radii
+> size =sel stickRadius 0.14
+Changed 3 bond radii
+> size =sel stickRadius 0.13
+Changed 3 bond radii
+> size =sel stickRadius 0.12
+Changed 3 bond radii
+> size =sel stickRadius 0.11
+Changed 3 bond radii
+> size =sel stickRadius 0.1
+Changed 3 bond radii
+> size =sel stickRadius 0.11
+Changed 3 bond radii
+> size =sel stickRadius 0.12
+Changed 3 bond radii
+> size =sel stickRadius 0.13
+Changed 3 bond radii
+> size =sel stickRadius 0.14
+Changed 3 bond radii
+> size =sel stickRadius 0.15
+Changed 3 bond radii
+> size =sel stickRadius 0.14
+Changed 3 bond radii
+> size =sel stickRadius 0.13
+Changed 3 bond radii
+> size =sel stickRadius 0.12
+Changed 3 bond radii
+> size =sel stickRadius 0.11
+Changed 3 bond radii
+> size =sel stickRadius 0.1
+Changed 3 bond radii
+> size =sel stickRadius 0.09
+Changed 3 bond radii
+> size =sel stickRadius 0.08
+Changed 3 bond radii
+> size =sel stickRadius 0.09
+Changed 3 bond radii
+> size =sel stickRadius 0.1
+Changed 3 bond radii
+> size =sel stickRadius 0.11
+Changed 3 bond radii
+> size =sel stickRadius 0.12
+Changed 3 bond radii
+> size =sel stickRadius 0.13
+Changed 3 bond radii
+> size =sel stickRadius 0.14
+Changed 3 bond radii
+> size =sel stickRadius 0.15
+Changed 3 bond radii
+> size =sel stickRadius 0.16
+Changed 3 bond radii
+> size =sel stickRadius 0.17
+Changed 3 bond radii
+> size =sel stickRadius 0.18
+Changed 3 bond radii
+> size =sel stickRadius 0.19
+Changed 3 bond radii
+> size =sel stickRadius 0.2
+Changed 3 bond radii
+> select clear
+> select add #5/B:34@DD2
+atom, 2 bonds, 1 residue, 1 model selected
+> select add #5/B:163@ND1
+atoms, 3 bonds, 2 residues, 1 model selected
+> select subtract #5/B:163@ND1
+atom, 3 bonds, 1 residue, 1 model selected
+> ui tool show "Selection Inspector"
+> size =sel stickRadius 0.19
+Changed 6 bond radii
+> size =sel stickRadius 0.18
+Changed 6 bond radii
+> size =sel stickRadius 0.17
+Changed 6 bond radii
+> size =sel stickRadius 0.16
+Changed 6 bond radii
+> size =sel stickRadius 0.15
+Changed 6 bond radii
+> size =sel stickRadius 0.14
+Changed 6 bond radii
+> size =sel stickRadius 0.13
+Changed 6 bond radii
+> size =sel stickRadius 0.12
+Changed 6 bond radii
+> size =sel stickRadius 0.11
+Changed 6 bond radii
+> size =sel stickRadius 0.12
+Changed 6 bond radii
+> select subtract #5/B:34@DD2
+bonds, 1 model selected
+> size =sel stickRadius 0.12
+Changed 7 bond radii
+> select add #5/B:30@DD2
+atom, 14 bonds, 1 residue, 1 model selected
+> select subtract #5/B:30@DD2
+bonds, 1 model selected
+> select add #5/B:30@DD2
+atom, 14 bonds, 1 residue, 1 model selected
+> select add #5/D:166@DE2
+atoms, 16 bonds, 2 residues, 1 model selected
+> select subtract #5/D:166@DE2
+atom, 16 bonds, 1 residue, 1 model selected
+> select add #5/D:166@DE2
+atoms, 16 bonds, 2 residues, 1 model selected
+> select subtract #5/D:166@DE2
+atom, 16 bonds, 1 residue, 1 model selected
+> select add #5/D:166@DE2
+atoms, 17 bonds, 2 residues, 1 model selected
+> select subtract #5/D:166@DE2
+atom, 17 bonds, 1 residue, 1 model selected
+> size =sel stickRadius 0.12
+Changed 19 bond radii
+> select subtract #5/B:30@DD2
+bonds, 1 model selected
+> select add #5/B:30@DD2
+atom, 19 bonds, 1 residue, 1 model selected
+> select subtract #5/B:30@DD2
+bonds, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr =sel b display false
+Assigning display attribute to 21 items
+> setattr =sel b display true
+Assigning display attribute to 21 items
+Cannot increment value
+> select clear
+> ui tool show "Selection Inspector"
+> size =sel stickRadius 0.19
+Changed 1 bond radii
+> size =sel stickRadius 0.12
+Changed 1 bond radii
+> select add #5/B:30@DB2
+atom, 1 bond, 1 residue, 1 model selected
+> select clear
+> select #5/b,d & main & @D* & @@display
+atoms, 23 residues, 1 model selected
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/sel_bonds.py" format
+> python
+executed sel_bonds.py
+> ui tool show "Selection Inspector"
+> size =sel stickRadius 0.12
+Changed 133 bond radii
+> select clear
+> select #5/b,d & main & @D* & @@display
+atoms, 23 residues, 1 model selected
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/sel_bonds.py"
+executed sel_bonds.py
+> ui tool show "Selection Inspector"
+> name frozen ox_H_atomic-bonds
+Missing or invalid "objects" argument: empty atom specifier
+> name frozen ox_H_atomic-bonds sel
+> ui tool show "Selection Inspector"
+> size =sel stickRadius 0.13
+Changed 134 bond radii
+> size =sel stickRadius 0.14
+Changed 134 bond radii
+> size =sel stickRadius 0.13
+Changed 134 bond radii
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site_red, session-start, wat1-q143, y166-h30
+> view active-site
+> view active-site-1
+> view active-site
+> view active-site-2
+> view active-site_red
+> view active-site-3
+> select clear
+> select #5/B:77
+atoms, 20 bonds, 1 residue, 1 model selected
+> view active-site_red
+> view active-site-3
+> view active-site-2
+[Repeated 1 time(s)]
+> select clear
+> view active-site-2
+> view active-site-3
+[Repeated 1 time(s)]
+> select clear
+> select #5/B:76
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #5/B:76
+atoms, 18 bonds, 1 residue, 1 model selected
+> select clear
+[Repeated 1 time(s)]
+> select #5/B:77
+atoms, 20 bonds, 1 residue, 1 model selected
+> select clear
+> view active-site-1
+> select clear
+> view name active-site-2
+> select clear
+> ui mousemode right pivot
+[Repeated 1 time(s)]
+> ui mousemode right translate
+> lighting DepthCue false
+Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
+keyword
+> lighting depthCue false
+> lighting depthCue true
+> lighting depthCueStart 0.75
+> lighting depthCueStart 0.6
+> lighting depthCueStart 0.5
+> lighting depthCueStart 0.7
+> lighting depthCueStart 0.75
+> select #5/D:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select clear
+> hide #!5 atoms
+> undo
+> select clear
+[Repeated 1 time(s)]
+> select #5/D:162@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 14 bonds, 1 residue, 1 model selected
+> select sel & ~sidechain
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> view name active-site-4
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site-4, active-site_red, session-start, wat1-q143, y166-h30
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site-4
+[Repeated 1 time(s)]
+> view name active-site-3
+> view active-site-4
+> view active-site-3
+> view active-site-4
+> view active-site-3
+> view name active-site-5
+> view lisr
+Expected an objects specifier or a view name or a keyword
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site-4, active-site-5, active-site_red, session-start, wat1-q143, y166-h30
+> view active-site-5
+[Repeated 2 time(s)]
+> select #5/B:66
+atoms, 20 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select clear
+> select #5/D:171
+atoms, 13 bonds, 1 residue, 1 model selected
+> select add #5/D:170
+atoms, 34 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select #5/B:161@N
+atom, 1 residue, 1 model selected
+> ui tool show "Selection Inspector"
+> size sel atomRadius 1.2
+Changed 1 atom radii
+> style sel ball
+Changed 1 atom style
+> size sel atomRadius 1.2
+Changed 1 atom radii
+> size sel atomRadius 1.19
+Changed 1 atom radii
+> size sel atomRadius 1.18
+Changed 1 atom radii
+> size sel atomRadius 1.17
+Changed 1 atom radii
+> size sel atomRadius 1.16
+Changed 1 atom radii
+> size sel atomRadius 1.15
+Changed 1 atom radii
+> size sel atomRadius 1.14
+Changed 1 atom radii
+> size sel atomRadius 1.13
+Changed 1 atom radii
+> size sel atomRadius 1.12
+Changed 1 atom radii
+> size sel atomRadius 1.11
+Changed 1 atom radii
+> size sel atomRadius 1.1
+Changed 1 atom radii
+> size sel atomRadius 1.09
+Changed 1 atom radii
+> size sel atomRadius 1.08
+Changed 1 atom radii
+> size sel atomRadius 1.07
+Changed 1 atom radii
+> size sel atomRadius 1.06
+Changed 1 atom radii
+> size sel atomRadius 1.05
+Changed 1 atom radii
+> size sel atomRadius 1.04
+Changed 1 atom radii
+> size sel atomRadius 1.03
+Changed 1 atom radii
+> size sel atomRadius 1.02
+Changed 1 atom radii
+> size sel atomRadius 1.01
+Changed 1 atom radii
+> size sel atomRadius 1
+Changed 1 atom radii
+> size sel atomRadius 0.99
+Changed 1 atom radii
+> size sel atomRadius 0.98
+Changed 1 atom radii
+> size sel atomRadius 0.97
+Changed 1 atom radii
+> size sel atomRadius 0.96
+Changed 1 atom radii
+> size sel atomRadius 0.95
+Changed 1 atom radii
+> size sel atomRadius 0.94
+Changed 1 atom radii
+> size sel atomRadius 0.93
+Changed 1 atom radii
+> size sel atomRadius 0.92
+Changed 1 atom radii
+> size sel atomRadius 0.6
+Changed 1 atom radii
+> hide sel atoms
+> show sel atoms
+> select clear
+> select ox_H_atomic-bonds
+atoms, 134 bonds, 23 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> size =sel stickRadius 0.12
+Changed 134 bond radii
+> size =sel stickRadius 0.13
+Changed 134 bond radii
+> size =sel stickRadius 0.12
+Changed 134 bond radii
+> size =sel stickRadius 0.13
+Changed 134 bond radii
+> size =sel stickRadius 0.12
+Changed 134 bond radii
+> size =sel stickRadius 0.11
+Changed 134 bond radii
+> size =sel stickRadius 0.1
+Changed 134 bond radii
+> size =sel stickRadius 0.11
+Changed 134 bond radii
+> size =sel stickRadius 0.12
+Changed 134 bond radii
+> size =sel stickRadius 0.13
+Changed 134 bond radii
+> size =sel stickRadius 0.12
+Changed 134 bond radii
+> select clear
+> view name active-site
+[Repeated 1 time(s)]
+> view active-site
+[Repeated 1 time(s)]
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini
+> review/Figs_V3/MnSOD_Ox_full.tif" width 1291 height 859 supersample 3
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> select clear
+> select #5/B:34@OH
+atom, 1 residue, 1 model selected
+> ui mousemode right distance
+> distance #5/B:161@CD2 #5/B:34@OH
+Distance between combination #5/B TRP 161 CD2 and TYR 34 OH: 4.828Å
+> show #!4 models
+> close #4
+> distance #5/B:143@DE22 #5/B:34@OH
+Distance between combination #5/B GLN 143 DE22 and TYR 34 OH: 2.014Å
+> close #4
+> select #5/B:143@DE22
+atom, 1 residue, 1 model selected
+> select add #5/B:34@OH
+atoms, 2 residues, 1 model selected
+> pbond sel color cyan
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini
+> review/Figs_V3/MnSOD_Ox_full.tif" width 1291 height 859 supersample 3
+> select #5/B:73@CB
+atom, 1 residue, 1 model selected
+> select add #5/B:161@D
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 38 bonds, 2 residues, 1 model selected
+> select clear
+> show #!3 models
+> hide #!5 models
+> distance #3/B:30@DD1 #3/B:348@O
+Distance between combination #3/B HIS 30 DD1 and DOD 348 O: 2.922Å
+> ui mousemode right "move label"
+> ui mousemode right distance
+> distance #3/B:348@O #3/B:566@D
+Distance between combination #3/B DOD 348 O and D8U 566 D: 2.878Å
+> hide #!4 models
+> close #4
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> distance #5/B:34@OH #5/B:143@DE22
+Distance between combination #5/B TYR 34 OH and GLN 143 DE22: 2.014Å
+> distance #5/B:30@ND1 #5/B:347@D1
+Distance between combination #5/B HIS 30 ND1 and HOH 347 D1: 2.690Å
+> close #4
+> show #!3 models
+> hide #!5 models
+> select #3/B:566@D
+atom, 1 residue, 1 model selected
+> select clear
+[Repeated 1 time(s)]
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!3 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 atoms
+> undo
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> distance #3/B:34@OH #3/B:143@DE22
+Distance between combination #3/B TYR 34 OH and GLN 143 DE22: 1.700Å
+> distance #3/B:319@D2 #3/B:143@NE2
+Distance between combination #3/B DOD 319 D2 and GLN 143 NE2: 1.594Å
+> distance #3/B:123@DE1 #3/B:143@OE1
+Distance between combination #3/B TRP 123 DE1 and GLN 143 OE1: 1.482Å
+> show #!2 models
+> hide #!3 models
+> distance #2.1/A:143@DE22 #2.1/A:34@OH
+Distance between MnSOD_red #2.1/A GLN 143 DE22 and TYR 34 OH: 2.184Å
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!2 models
+> show #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/Figs_V3/MnSOD_Red_SSHB-
+> dist.tif" width 1291 height 859 supersample 3
+> view active-site
+> hide #!4 models
+> select #3/b,d & @@display & ~sideonly
+atoms, 6 bonds, 1 pseudobond, 16 residues, 2 models selected
+> select #3/b,d & @@display & sideonly
+atoms, 114 bonds, 5 pseudobonds, 11 residues, 3 models selected
+> select #3/b,d & @@display & ~backbone
+atoms, 118 bonds, 14 pseudobonds, 15 residues, 6 models selected
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 interModel false distSlop 0.5 intraRes
+> false reveal true retainCurrent true
+hydrogen bonds found
+> select #3/D:306@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select #3/B:163@DA
+atom, 1 residue, 1 model selected
+> select #3/B:163@CG
+atom, 1 residue, 1 model selected
+> delete pbonds sel
+[Repeated 1 time(s)]
+> select clear
+> select #3/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #3/B:161@O
+atom, 1 residue, 1 model selected
+> select add #3/B:161@DA
+atoms, 1 bond, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #3/B:163@O
+atom, 1 residue, 1 model selected
+> select add #3/B:163@DA
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!5 models
+> select #3/B:163@D
+atom, 1 residue, 1 model selected
+> select add #3/D:335@O
+atoms, 2 residues, 1 model selected
+> select #3/D:335@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> select add #3/B:163@D
+atoms, 2 bonds, 2 residues, 1 model selected
+> select add #3/B:163@N
+atoms, 2 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> select #3/B:142@O
+atom, 1 residue, 1 model selected
+> select #3/B:142
+atoms, 13 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #3/B:30@C
+atom, 1 residue, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr sel r ribbon_hide_backbone true
+Assigning ribbon_hide_backbone attribute to 1 item
+> setattr sel r ribbon_hide_backbone false
+Assigning ribbon_hide_backbone attribute to 1 item
+> select #3/B:30@O
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> setattr sel r ribbon_hide_backbone true
+Assigning ribbon_hide_backbone attribute to 1 item
+> setattr sel r ribbon_hide_backbone false
+Assigning ribbon_hide_backbone attribute to 1 item
+> select #3/B:30@DA
+atom, 1 residue, 1 model selected
+> select add #3/B:30@C
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #3/B:70
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view active-site
+> show #!5 models
+> hide #!5 models
+> select #3/D:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select clear
+> view name active-site-red-2
+> view active-site-red-2
+[Repeated 1 time(s)]
+> ui tool show "Selection Inspector"
+> color =sel #00f900 pseudobonds
+> ui tool show "Color Actions"
+> color =sel lime pseudobonds
+> select clear
+> hide #5.3 models
+> show #5.3 models
+> hide #!5 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.6 models
+> hide #3.4 models
+> show #3.4 models
+> show #3.6 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.6 models
+> hide #3.4 models
+> show #3.4 models
+> hide #3.4 models
+> show #3.6 models
+> close #3.4
+> hide #3.5 models
+> show #3.5 models
+> hide #3.5 models
+> show #3.5 models
+> hide #3.5 models
+> show #3.5 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.6 models
+> show #3.6 models
+> select clear
+> delete pbonds sel
+> select #3/B:143@OE1
+atom, 1 residue, 1 model selected
+> select add #3/B:123@DE1
+atoms, 2 residues, 1 model selected
+> pbond sel
+> select #3/B:143@DE22
+atom, 1 residue, 1 model selected
+> select add #3/B:34@OH
+atoms, 2 residues, 1 model selected
+> pbond sel
+> select clear
+> undo
+[Repeated 1 time(s)]
+> select clear
+> hide #3.5 models
+> show #3.5 models
+> color #3.5 lime pseudobonds
+> style sel dashes 7
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 12
+Changed 1 pseudobond dash
+> setattr sel g radius 0.11
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.12
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.13
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.14
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.15
+Assigning radius attribute to 1 item
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> setattr sel g radius 0.14
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.13
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.12
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.11
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.1
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.11
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.12
+Assigning radius attribute to 1 item
+> setattr sel g radius 0.13
+Assigning radius attribute to 1 item
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 12
+Changed 1 pseudobond dash
+> style sel dashes 13
+Changed 1 pseudobond dash
+> style sel dashes 14
+Changed 1 pseudobond dash
+> style sel dashes 15
+Changed 1 pseudobond dash
+> style sel dashes 16
+Changed 1 pseudobond dash
+> style sel dashes 15
+Changed 1 pseudobond dash
+> style sel dashes 14
+Changed 1 pseudobond dash
+> style sel dashes 13
+Changed 1 pseudobond dash
+> style sel dashes 12
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> style sel dashes 7
+Changed 1 pseudobond dash
+> style sel dashes 6
+Changed 1 pseudobond dash
+> style sel dashes 7
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 12
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> select clear
+> view active-site-red-2
+> select /b,d & main & @D* & @@display
+atoms, 70 residues, 6 models selected
+> select /b,d & main & @D* & @@display & ##display
+atoms, 41 residues, 4 models selected
+> select clear
+> select /b,d & main & @D* & @@display & ##display
+atoms, 41 residues, 4 models selected
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!3 models
+> select /b,d & main & @D* & @@display & ##display
+atoms, 41 residues, 4 models selected
+> help help:user
+> select #3 & /b,d & main & @D* & @@display
+atoms, 11 residues, 1 model selected
+> name vis-D /b,d & main & @D* & @@display
+"/b,d & main & @D* & @@display ": contains extra trailing text
+> name vis-D /b,d & main & @D* & @@display
+> select clear
+> select #3 vis-D
+Expected a keyword
+> select #3 & vis-D
+atoms, 11 residues, 1 model selected
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/sel_bonds.py"
+executed sel_bonds.py
+> size =sel stickRadius 0.19
+Changed 61 bond radii
+> size =sel stickRadius 0.18
+Changed 61 bond radii
+> size =sel stickRadius 0.17
+Changed 61 bond radii
+> size =sel stickRadius 0.16
+Changed 61 bond radii
+> size =sel stickRadius 0.15
+Changed 61 bond radii
+> size =sel stickRadius 0.14
+Changed 61 bond radii
+> size =sel stickRadius 0.13
+Changed 61 bond radii
+> size =sel stickRadius 0.12
+Changed 61 bond radii
+> size =sel stickRadius 0.13
+Changed 61 bond radii
+> size =sel stickRadius 0.14
+Changed 61 bond radii
+> show #!5 models
+> select clear
+> hide #!5 models
+> select #3 & vis-D
+atoms, 11 residues, 1 model selected
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/sel_bonds.py"
+executed sel_bonds.py
+> name list
+CDs @D* & ((C & @@display) @< 1.5)
+ox_H_atomic-bonds [133 atoms, 134 bonds]
+sh-o [482 atoms, 466 bonds, 5 models]
+sh-r [627 atoms, 610 bonds, 4 models]
+vis-D /b,d & main & @D* & @@display
+> size =sel stickRadius 0.13
+Changed 61 bond radii
+> size =sel stickRadius 0.12
+Changed 61 bond radii
+> name frozen red_H_atomic-bonds sel
+> select red_H_atomic-bonds
+atoms, 61 bonds, 11 residues, 1 model selected
+> select add #3/B:566@D
+atoms, 62 bonds, 12 residues, 1 model selected
+> name frozen red_H_atomic-bonds sel
+> size =sel stickRadius 0.19
+Changed 1 bond radii
+> size =sel stickRadius 0.18
+Changed 1 bond radii
+> size =sel stickRadius 0.17
+Changed 1 bond radii
+> size =sel stickRadius 0.16
+Changed 1 bond radii
+> size =sel stickRadius 0.15
+Changed 1 bond radii
+> size =sel stickRadius 0.14
+Changed 1 bond radii
+> size =sel stickRadius 0.13
+Changed 1 bond radii
+> size =sel stickRadius 0.12
+Changed 1 bond radii
+> select clear
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site-4, active-site-5, active-site-red-2, active-site_red, session-start,
+wat1-q143, y166-h30
+> view active-site_red
+> view active-site-red-2
+> view active-site_red
+> view active-site-red-2
+> view active-site_red
+> view active-site-red-2
+> view active-site_red
+> view active-site-red-2
+[Repeated 2 time(s)]
+> ui mousemode right pivot
+> view active-site-red-2
+> view name active-site-red-3
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site-4, active-site-5, active-site-red-2, active-site-red-3, active-site_red,
+session-start, wat1-q143, y166-h30
+> view active-site_red
+> view active-site-red-2
+> view active-site-red-3
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini
+> review/Figs_V3/MnSOD_Red_full_3-SSHB.tif" width 1291 height 859 supersample
+> 3
+> setattr =sel p display false
+Assigning display attribute to 1 item
+> select #3/B:143@DE22
+atom, 1 residue, 1 model selected
+> select add #3/B:34@OH
+atoms, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #00fdff dashes 6 restrict both interModel false distSlop
+> 0.5 intraRes false reveal true retainCurrent true
+hydrogen bonds found
+> pbond sel color cyan name H-bond
+> select clear
+> view active-site-red-3
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini
+> review/Figs_V3/MnSOD_Red_full_2-SSHB.tif" width 1291 height 859 supersample
+> 3
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.4 models
+> select #3/B:143@DE22
+atom, 1 residue, 1 model selected
+> select #3/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #3/B:143@DE22
+atoms, 2 residues, 1 model selected
+> show #3.4 models
+> select add #3.5
+atoms, 3 pseudobonds, 2 residues, 2 models selected
+> style sel dashes 7
+Changed 3 pseudobond dashes
+> style sel dashes 6
+Changed 3 pseudobond dashes
+> setattr sel g radius 0.12
+Assigning radius attribute to 3 items
+> setattr sel g radius 0.11
+Assigning radius attribute to 3 items
+> setattr sel g radius 0.12
+Assigning radius attribute to 3 items
+> setattr sel g radius 0.11
+Assigning radius attribute to 3 items
+> setattr sel g radius 0.1
+Assigning radius attribute to 3 items
+> select clear
+> select add #3.5
+pseudobonds, 1 model selected
+> style sel dashes 5
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 5
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 5
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 3
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 3
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 5
+Changed 1 pseudobond dash
+> style sel dashes 6
+Changed 1 pseudobond dash
+> style sel dashes 7
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 11
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> style sel dashes 7
+Changed 1 pseudobond dash
+> style sel dashes 6
+Changed 1 pseudobond dash
+> style sel dashes 5
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 3
+Changed 1 pseudobond dash
+> style sel dashes 2
+Changed 1 pseudobond dash
+> style sel dashes 3
+Changed 1 pseudobond dash
+> style sel dashes 4
+Changed 1 pseudobond dash
+> style sel dashes 5
+Changed 1 pseudobond dash
+> style sel dashes 6
+Changed 1 pseudobond dash
+> style sel dashes 7
+Changed 1 pseudobond dash
+> style sel dashes 8
+Changed 1 pseudobond dash
+> style sel dashes 9
+Changed 1 pseudobond dash
+> style sel dashes 10
+Changed 1 pseudobond dash
+> setattr sel g color #ff9300
+Assigning color attribute to 1 item
+> setattr sel g color #ff40ff
+Assigning color attribute to 1 item
+> setattr sel g color #ff9300
+Assigning color attribute to 1 item
+> setattr sel g color #942192
+Assigning color attribute to 1 item
+> setattr sel g color #ff2600
+Assigning color attribute to 1 item
+> setattr sel g color #ff9300
+Assigning color attribute to 1 item
+> ui tool show "Color Actions"
+> hide #!3 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!2 models
+> cofr sel
+No displayed objects specified.
+> select clear
+> cofr frontCenter
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> ui mousemode right distance
+> distance #1.1/B:30@ND1 #1.1/B:347@D1
+Distance between MnSOD_ox #1.1/B HIS 30 ND1 and HOH 347 D1: 2.690Å
+> select clear
+> cofr frontCenter
+> select #1.1/A:34
+atoms, 20 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #1.1/A:123@DE3
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select #1.1/A:66@DZ
+atom, 1 residue, 1 model selected
+> select up
+atoms, 20 bonds, 1 residue, 1 model selected
+> show sel atoms
+> hide sel atoms
+> distance #1.1/A:30@DD1 #1.1/A:306@O
+Distance between MnSOD_ox #1.1/A HIS 30 DD1 and HOH 306 O: 2.215Å
+> distance #1.1/A:306@O #1.1/A:34@OH
+Distance between MnSOD_ox #1.1/A HOH 306 O and TYR 34 OH: 2.278Å
+> distance #1.1/A:30@ND1 #1.1/A:306@O
+Distance between MnSOD_ox #1.1/A HIS 30 ND1 and HOH 306 O: 3.146Å
+> undo
+> redo
+> delete pbonds sel
+> show #!2 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> distance #2.1/B:34@OH #2.1/B:566@D
+Distance between MnSOD_red #2.1/B TYR 34 OH and D8U 566 D: 1.295Å
+> distance #2.1/B:66@DE2 #2.1/B:66@CE2
+Distance between MnSOD_red #2.1/B PHE 66 DE2 and CE2: 1.080Å
+> show #!1 models
+> hide #!2 models
+> distance #1.1/A:34@OH #1.1/A:143@DE22
+Distance between MnSOD_ox #1.1/A TYR 34 OH and GLN 143 DE22: 2.327Å
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> view active-site-red-3
+> show #!3 models
+> hide #!4 models
+> hide #!1 models
+> hide #!5 models
+> hide #3.2 models
+> show #3.2 models
+> hide #3.4 models
+> show #3.4 models
+> hide #3.6 models
+> show #3.6 models
+> hide #3.6 models
+> show #3.6 models
+> color #3.6 black models
+> color #3.6 #00fdffff models
+> color sel black target pbonds
+Invalid "target" argument: Character 'o' is not an allowed target, must be one
+of acrsbmpfl
+> color sel black target p
+> select clear
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> show #!5 models
+> hide #!3 models
+> distance #5/B:30@NE2 #5/B:30@HE2
+Distance between combination #5/B HIS 30 NE2 and HE2: 1.711Å
+> show #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> distance #5/B:143@DE22 #5/B:34@OH
+Distance between combination #5/B GLN 143 DE22 and TYR 34 OH: 2.014Å
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> distance #5/D:166@OH #5/B:30@NE2
+Distance between combination #5/D TYR 166 OH and /B HIS 30 NE2: 2.728Å
+> distance #5/B:143@NE2 #5/B:34@OH
+Distance between combination #5/B GLN 143 NE2 and TYR 34 OH: 2.724Å
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!5 models
+> show #!5 models
+> show #!3 models
+> hide #!4 models
+> show #!4 models
+> hide #!3 models
+> distance #5/B:123@DE1 #5/B:143@OE1
+Distance between combination #5/B TRP 123 DE1 and GLN 143 OE1: 1.850Å
+> distance #5/B:143@OE1 #5/B:73@DD21
+Distance between combination #5/B GLN 143 OE1 and ASN 73 DD21: 2.549Å
+> distance #5/D:162@OE2 #5/B:163@DD1
+Distance between combination #5/D GLU 162 OE2 and /B HIS 163 DD1: 1.948Å
+> distance #5/B:336@D1 #5/B:34@OH
+Distance between combination #5/B HOH 336 D1 and TYR 34 OH: 2.139Å
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site-4, active-site-5, active-site-red-2, active-site-red-3, active-site_red,
+session-start, wat1-q143, y166-h30
+> distance #5/B:143@OE1 #5/B:73@ND2
+Distance between combination #5/B GLN 143 OE1 and ASN 73 ND2: 3.564Å
+> select #5/B:73
+atoms, 13 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> distance #5/B:161@D #5/B:159@OD1
+Distance between combination #5/B TRP 161 D and ASP 159 OD1: 2.346Å
+> distance #5/B:161@N #5/B:159@OD1
+Distance between combination #5/B TRP 161 N and ASP 159 OD1: 3.301Å
+> distance #5/B:347@D2 #5/B:336@O
+Distance between combination #5/B HOH 347 D2 and HOH 336 O: 1.614Å
+> distance #5/B:347@O #5/B:336@O
+Distance between combination #5/B HOH 347 O and HOH 336 O: 2.307Å
+> distance #5/B:30@ND1 #5/B:347@D1
+Distance between combination #5/B HIS 30 ND1 and HOH 347 D1: 2.690Å
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> ui tool show Angles/Torsions
+> select #5/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #5/B:30@HE2
+atoms, 2 residues, 1 model selected
+> select add #5/B:30@NE2
+atoms, 2 residues, 1 model selected
+> show #!4 models
+> show #!3 models
+> hide #!5 models
+> ui mousemode right "translate selected atoms"
+> ui mousemode right translate
+> ui mousemode right "move label"
+> ui mousemode right distance
+> ~distance #5/B:143@NE2 #5/B:34@OH
+> ~distance #2.1/A:143@DE22 #2.1/A:34@OH
+> distance #3/B:34@OH #3/B:143@NE2
+Distance between combination #3/B TYR 34 OH and GLN 143 NE2: 2.538Å
+> select #3/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #3/B:143@DE22
+atoms, 2 residues, 1 model selected
+> select add #3/B:143@NE2
+atoms, 2 residues, 1 model selected
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> hide #!4 models
+> color #3.4 #00fdffff models
+> select clear
+> select add #3.5
+pseudobonds, 1 model selected
+> setattr sel g display false
+Assigning display attribute to 1 item
+> setattr sel g display true
+Assigning display attribute to 1 item
+> setattr =sel p display true
+Assigning display attribute to 3 items
+> setattr =sel p display false
+Assigning display attribute to 3 items
+> setattr =sel p display true
+Assigning display attribute to 3 items
+> hide #3.6 models
+> show #3.6 models
+> hide #3.4 models
+> color sel darkred sky blue target p
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color sel darkskyblue target p
+Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
+'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
+'fromcartoons', 'fromribbons', or 'random' or a keyword
+> ui tool show "Color Actions"
+> color sel deeppink skycblue target p
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color sel deep sky blue target p
+> select clear
+> view list
+Named views: active-site, active-site-1, active-site-2, active-site-3, active-
+site-4, active-site-5, active-site-red-2, active-site-red-3, active-site_red,
+session-start, wat1-q143, y166-h30
+> view active-site-red-3
+> view active-site-red-2
+> view active-site-red-3
+> view active-site-red-2
+> view active-site-red-3
+> view active-site-red-2
+> view active-site-red-3
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> distance #3/B:159@OD1 #3/B:161@D
+Distance between combination #3/B ASP 159 OD1 and TRP 161 D: 2.224Å
+> distance #3/B:159@OD1 #3/B:161@N
+Distance between combination #3/B ASP 159 OD1 and TRP 161 N: 3.211Å
+> distance #3/B:159@OD1 #3/B:319@D1
+Distance between combination #3/B ASP 159 OD1 and DOD 319 D1: 2.512Å
+> hide #!4 models
+> select #3/B:30@D
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #3/B:30
+atoms, 17 bonds, 1 residue, 1 model selected
+> setattr sel r ribbon_hide_backbone true
+Assigning ribbon_hide_backbone attribute to 1 item
+> setattr sel r ribbon_hide_backbone false
+Assigning ribbon_hide_backbone attribute to 1 item
+> select clear
+> view active-site-red-2
+> view active-site-red-3
+> view active-site-red-2
+> view active-site-red-3
+> view active-site-red-2
+> view active-site-red-3
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> hide #!3 models
+> show #!5 models
+> view active-site-5
+> view active-site-4
+> view active-site-5
+> view active-site-red-3
+> view active-site-5
+> view active-site-red-3
+> view active-site-4
+> view active-site-red-3
+> view active-site-5
+> show #!3 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> view active-site-red-3
+> view active-site-red-2
+> view active-site-red-3
+[Repeated 2 time(s)]
+> view active-site-5
+> view active-site-red-3
+> show #!5 models
+> hide #!3 models
+> view active-site-5
+> view active-site-red-2
+> view active-site-5
+> view active-site-red-3
+> view active-site-5
+> view active-site-4
+> view active-site-3
+> view active-site-2
+> view active-site-1
+> view active-site-2
+> view active-site-4
+> view active-site-5
+> view active-site-1
+> view active-site-2
+> view active-site-5
+> view active-site-2
+> view active-site-3
+> view active-site-4
+> view active-site-2
+> view active-site-4
+> view active-site-2
+> view active-site-4
+> view active-site-2
+> view active-site-5
+> view active-site-red-3
+> view active-site-5
+> view active-site-red-3
+> select #5/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #5/B:161@N
+atom, 1 residue, 1 model selected
+> select add #5/B:161@D
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view active-site-5
+> view active-site-red-3
+> view active-site-5
+[Repeated 2 time(s)]
+> view active-site-red-3
+> view active-site-5
+> view active-site-red-3
+> show #!3 models
+> hide #!3 models
+> view active-site-5
+[Repeated 1 time(s)]
+> view active-site
+> view active-site-5
+> view active-site
+> view active-site-red-3
+> view active-site
+> view active-site-red-3
+> view active-site
+> show #!3 models
+> hide #!5 models
+> view active-site-red-3
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> hide #!3 models
+> show #!5 models
+> select #5.1,3
+pseudobonds, 2 models selected
+> color sel deep sky blue target p
+> select clear
+> ui mousemode right label
+> ui mousemode right distance
+> close #4
+> distance #5/B:30@ND1 #5/B:347@D1
+Distance between combination #5/B HIS 30 ND1 and HOH 347 D1: 2.690Å
+> hide #!4 models
+> show #!4 models
+> select add #4
+pseudobonds, 3 models selected
+> select add #5
+atoms, 13165 bonds, 32 pseudobonds, 1050 residues, 6 models selected
+> select subtract #5
+model selected
+> select add #4
+pseudobond, 2 models selected
+> close #4
+> show #!3 models
+> hide #!5 models
+> distance #3/B:34@OH #3/B:143@NE2
+Distance between combination #3/B TYR 34 OH and GLN 143 NE2: 2.538Å
+> distance #3/D:166@OH #3/B:30@NE2
+Distance between combination #3/D TYR 166 OH and /B HIS 30 NE2: 2.443Å
+> hide #!3 models
+> show #!5 models
+> distance #5/D:166@OH #5/B:30@NE2
+Distance between combination #5/D TYR 166 OH and /B HIS 30 NE2: 2.728Å
+> distance #5/B:34@OH #5/B:143@NE2
+Distance between combination #5/B TYR 34 OH and GLN 143 NE2: 2.724Å
+> hide #!4 models
+> show #!4 models
+> show #!3 models
+> hide #!4 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!3 models
+> label sel
+> select #5/B:30
+atoms, 16 bonds, 1 pseudobond, 1 residue, 2 models selected
+> select #5/B:30
+atoms, 16 bonds, 1 pseudobond, 1 residue, 2 models selected
+> select add #5.3.1
+pseudobond, 2 models selected
+> show #!3 models
+> hide #!5 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!4 models
+> show #!5 models
+> hide #!5 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!3 models
+> hide #5.3.1 models
+> show #!4 models
+> distance #5/B:336@D1 #5/B:34@OH
+Distance between combination #5/B HOH 336 D1 and TYR 34 OH: 2.139Å
+> distance #5/B:143@DE22 #5/B:34@OH
+Distance between combination #5/B GLN 143 DE22 and TYR 34 OH: 2.014Å
+> show #!3 models
+> hide #!5 models
+> hide #!4 models
+> distance #3/D:166@OH #3/B:30@NE2
+Distance already exists; modify distance properties with 'distance style'
+> show #!4 models
+> hide #!4 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/Figs_V3/MnSOD.cxs"
+——— End of log from Wed Aug 27 15:43:32 2025 ———
+> view name session-start
+opened ChimeraX session
+> close #4
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> hide #!2 models
+> show #!2 models
+> show #!1 models
+> hide #!1 models
+> hide #!2 models
+> show #!3 models
+> show #!5 models
+> hide #!3 models
+> hide #!5 models
+> show #!1 models
+> hide #!1.2 models
+> show #!1.2 models
+> hide #!1 models
+> show #!3 models
+> show #!5 models
+> rename #5 Oxidized id 4
+> rename #3 Reduced
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/Figs_V3/MnSOD.cxs"
+——— End of log from Wed Aug 27 15:48:40 2025 ———
+> view name session-start
+opened ChimeraX session
+> select clear
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_W161F.cxs" format
+> session combine true
+Not registering illegal selector name "carbon Ds"
+Log from Tue Aug 19 16:03:40 2025UCSF ChimeraX version: 1.10 (2025-06-26)
+© 2016-2025 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_fin.cxs" format
+> session
+Not registering illegal selector name "carbon Ds"
+Log from Fri Aug 15 23:42:37 2025UCSF ChimeraX version: 1.10 (2025-06-26)
+© 2016-2025 Regents of the University of California. All rights reserved.
+> surface cap true
+Not registering illegal selector name "carbon Ds"
+Log from Sun Apr 27 12:08:58 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_WIP.cxs"
+Not registering illegal selector name "carbon Ds"
+Log from Fri Apr 25 16:51:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+Not registering illegal selector name "carbon Ds"
+Log from Fri Apr 25 14:20:33 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+Log from Fri Apr 25 13:02:38 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox.cxs"
+Log from Thu Apr 24 19:50:15 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 Active
+> site_3.cxs"
+Log from Thu Apr 24 12:40:38 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+> format session
+Log from Mon Apr 21 17:37:05 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active stie.cxs"
+> format session
+Log from Fri Apr 18 13:46:35 2025UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 Active site.cxs"
+> format session
+Log from Fri Apr 18 13:15:54 2025 Startup Messages
+---
+note | available bundle cache has not been initialized yet
+You can double click a model's Name or ID in the model panel to edit those
+fields
+UCSF ChimeraX version: 1.9 (2024-12-11)
+© 2016-2024 Regents of the University of California. All rights reserved.
+How to cite UCSF ChimeraX
+> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/Xtalography/SSRL
+> FeSOD2/Oxidized/KMnO4_rinsed/Refine_34/KMnO4_rinsed_refine_034.pdb" format
+> pdb
+Chain information for KMnO4_rinsed_refine_034.pdb #1
+---
+Chain | Description
+A B | No description available
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+Computing secondary structure
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add sel @< 10
+atoms, 372 bonds, 57 residues, 1 model selected
+> select clear
+[Repeated 1 time(s)]
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select sel @< 5
+atoms, 37 bonds, 12 residues, 1 model selected
+> show sel atoms
+> select up
+atoms, 176 bonds, 12 residues, 1 model selected
+> show sel atoms
+> select /A:71
+atoms, 17 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> lighting simple
+> lighting soft
+> lighting full
+> lighting simple
+> ui tool show "Side View"
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select /A:163@NE2
+atom, 1 residue, 1 model selected
+> select add /D:4@FE
+atoms, 2 residues, 1 model selected
+> select clear
+> select #0:
+Expected an objects specifier or a keyword
+> select #0:a
+Nothing selected
+> select #0:A
+Nothing selected
+> select #0:b
+Nothing selected
+> select #0:H
+Nothing selected
+> select @H
+atoms, 372 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+[Repeated 1 time(s)]
+> show sel atoms
+> delete atoms sel
+> delete bonds sel
+> select @H*
+atoms, 396 residues, 1 model selected
+> hide sel atoms
+> select clear
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> view sel
+> ui tool show H-Bonds
+> hbonds reveal true
+hydrogen bonds found
+> undo
+> redo
+> ~hbonds
+> hbonds sel reveal true
+hydrogen bonds found
+> ui tool show H-Bonds
+> hbonds sel reveal true
+hydrogen bonds found
+> select /E:2@O
+atom, 1 residue, 1 model selected
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select sel @< 5
+atoms, 37 bonds, 12 residues, 1 model selected
+> select up
+atoms, 166 bonds, 12 residues, 1 model selected
+> select ~sel
+atoms, 5742 bonds, 1086 residues, 1 model selected
+> hide sel atoms
+> select ~sel & ##selected
+atoms, 184 bonds, 12 residues, 1 model selected
+> select @H*
+atoms, 396 residues, 1 model selected
+> hide sel atoms
+> select clear
+> select /E:2@O
+atom, 1 residue, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel reveal true
+hydrogen bonds found
+> select @H*
+atoms, 396 residues, 1 model selected
+> delete atoms sel
+> delete bonds sel
+> select clear
+> select /E:2@O
+atom, 1 residue, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel reveal true
+hydrogen bonds found
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select /A:163@NE2
+atom, 1 residue, 1 model selected
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add /A:163@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add /A:26@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add /A:74@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add /A:159@OD2
+atoms, 2 residues, 1 model selected
+> pbond sel
+> ui tool show "Selection Inspector"
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 4 items
+> setattr =sel p halfbond false
+Assigning halfbond attribute to 4 items
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 4 items
+> setattr =sel p display false
+Assigning display attribute to 4 items
+> setattr =sel p display true
+Assigning display attribute to 4 items
+> help help:user/tools/inspector.html
+> style sel stick dashes 0
+Changed 0 atom styles, 1 pseudobond dash
+> ui tool show "Selection Inspector"
+> size =sel pseudobondRadius 0.085
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.095
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.105
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.115
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.125
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.135
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.145
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.165
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.175
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.165
+Changed 4 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 4 pseudobond radii
+> select clear
+> select /A:143@CD
+atom, 1 residue, 1 model selected
+> select /A:123@NE1
+atom, 1 residue, 1 model selected
+> select add /A:143@CD
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 23 bonds, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel dashes 6 restrict both reveal true retainCurrent true
+hydrogen bonds found
+> select clear
+> select /A:34@CZ
+atom, 1 residue, 1 model selected
+> select /A:34@OH
+atom, 1 residue, 1 model selected
+> select add /A:30@ND1
+atoms, 2 residues, 1 model selected
+> select add /A:30@NE2
+atoms, 2 residues, 1 model selected
+> select add /A:163@ND1
+atoms, 3 residues, 1 model selected
+> select add /A:26@ND1
+atoms, 4 residues, 1 model selected
+> select add /A:74@ND1
+atoms, 5 residues, 1 model selected
+> select add /A:159@OD1
+atoms, 6 residues, 1 model selected
+> select add /A:161@NE1
+atoms, 7 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> select clear
+> select /S:229@O
+atom, 1 residue, 1 model selected
+> select add /S:12@O
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> hide sel
+> select clear
+> hide sel
+> select clear
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add /E:2@O
+atoms, 2 residues, 1 model selected
+> hbonds sel
+hydrogen bonds found
+> undo
+> select /A:143@NE2
+atom, 1 residue, 1 model selected
+> select add /S:263@O
+atoms, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> select /S:229@O
+atom, 1 residue, 1 model selected
+> select add /S:110@O
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> select /A:143@OE1
+atom, 1 residue, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> graphics silhouettes true
+> graphics silhouettes false
+> graphics silhouettes true
+> graphics silhouettes width 2
+> graphics silhouettes width 5
+> graphics silhouettes width 4
+> set bgColor white
+> hide sel
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> select add /E:2@O
+atoms, 2 residues, 1 model selected
+> pbond sel
+> style sel stick dashes 0
+Changed 0 atom styles, 1 pseudobond dash
+> select clear
+> ui tool show "Selection Inspector"
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 1 item
+> setattr =sel p halfbond false
+Assigning halfbond attribute to 1 item
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 1 item
+> size =sel pseudobondRadius 0.085
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.095
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.105
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.115
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.125
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.135
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.145
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.165
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.145
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.135
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.125
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.115
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.125
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.135
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.145
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.165
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.175
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.165
+Changed 1 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 1 pseudobond radii
+> select clear
+> ui tool show "Color Actions"
+> color #e5ffffff
+> color #e4ffffff
+> color #e3ffffff
+> color #d5ffffff
+> color #c0ffffff
+> color #a6ffffff
+> color #90ffffff
+> color #78ffffff
+> color #6effffff
+> color #60ffffff
+> color #55ffffff
+> color #51ffffff
+> color #4dffffff
+> color #4bffffff
+> color #49ffffff
+> color #47ffffff
+> color #43ffffff
+> color #41ffffff
+> color #40ffffff
+> color #3fffffff
+[Repeated 1 time(s)]
+> color #40ffffff
+> color #43ffffff
+> color #46ffffff
+> color #4dffffff
+> color #5affffff
+> color #63ffffff
+> color #6cffffff
+> color #76ffffff
+> color #89ffffff
+> color #98ffffff
+> color #a6ffffff
+> color #a9ffffff
+> color #bbffffff
+> color #c3ffffff
+> color #c8ffffff
+> color #d0ffffff
+> color #d6ffffff
+> color #daffffff
+> color #ddffffff
+> color #dfffffff
+> color #e1ffffff
+> color #e3ffffff
+> color #ecffffff
+> color #efffffff
+> color #f6ffffff
+> color #feffffff
+> color #ffffffff
+> color #5ce4cfff
+> color byhetero
+> color #96eee0ff
+> color byhetero
+> color #69e6d3ff
+> color byhetero
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting soft
+> lighting flat
+> lighting full
+> lighting shadows false
+> ui tool show "Selection Inspector"
+> select add /A:187
+atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected
+> select subtract /A:187
+pseudobonds, 1 model selected
+> select add /A:187
+atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected
+> select subtract /A:187
+pseudobonds, 1 model selected
+> ui tool show "Selection Inspector"
+> color =sel #69e6d4 pseudobonds
+> color =sel #69e6e5 pseudobonds
+> color =sel #69a3e6 pseudobonds
+> color =sel #6994e6 pseudobonds
+> color =sel #6984e6 pseudobonds
+> color =sel #6976e6 pseudobonds
+> color =sel #6970e6 pseudobonds
+> color =sel #696de6 pseudobonds
+> color =sel #696ae6 pseudobonds
+> color =sel #6d69e6 pseudobonds
+> color =sel #7169e6 pseudobonds
+> color =sel #7569e6 pseudobonds
+> color =sel #7969e6 pseudobonds
+> color =sel #7d69e6 pseudobonds
+> color =sel #8069e6 pseudobonds
+> color =sel #8369e6 pseudobonds
+> color =sel #8569e6 pseudobonds
+> color =sel #8769e6 pseudobonds
+> color =sel #8869e6 pseudobonds
+> color =sel #8a69e6 pseudobonds
+> color =sel #8b69e6 pseudobonds
+> color =sel #8c69e6 pseudobonds
+> color =sel #8e69e6 pseudobonds
+> color =sel #9269e6 pseudobonds
+> color =sel #c669e6 pseudobonds
+> color =sel #d269e6 pseudobonds
+> color =sel #e269e6 pseudobonds
+> color =sel #e669e1 pseudobonds
+> color =sel #e669d6 pseudobonds
+> color =sel #e669d2 pseudobonds
+> color =sel #e669c9 pseudobonds
+> color =sel #e669c6 pseudobonds
+> color =sel #e669c3 pseudobonds
+> color =sel #e669c1 pseudobonds
+> color =sel #e669be pseudobonds
+> color =sel #e669b9 pseudobonds
+> color =sel #e669b7 pseudobonds
+> color =sel #e669b8 pseudobonds
+> color =sel #e669ba pseudobonds
+> color =sel #e669bd pseudobonds
+> color =sel #e669e3 pseudobonds
+> color =sel #de69e6 pseudobonds
+> color =sel #d369e6 pseudobonds
+> color =sel #aa69e6 pseudobonds
+> color =sel #9669e6 pseudobonds
+> color =sel #8569e6 pseudobonds
+> color =sel #7d69e6 pseudobonds
+> color =sel #7569e6 pseudobonds
+> color =sel #6e69e6 pseudobonds
+> color =sel #696ce6 pseudobonds
+> color =sel #6972e6 pseudobonds
+> color =sel #697fe6 pseudobonds
+> color =sel #6983e6 pseudobonds
+> color =sel #6989e6 pseudobonds
+> color =sel #698fe6 pseudobonds
+> color =sel #6997e6 pseudobonds
+> color =sel #699fe6 pseudobonds
+> color =sel #69a8e6 pseudobonds
+> color =sel #69b1e6 pseudobonds
+> color =sel #69bbe6 pseudobonds
+> color =sel #69c7e6 pseudobonds
+> color =sel #69e6d9 pseudobonds
+> color =sel #69e6d0 pseudobonds
+> color =sel #69e6c5 pseudobonds
+> color =sel #69e6ba pseudobonds
+> color =sel #69e694 pseudobonds
+> color =sel #69e68c pseudobonds
+> color =sel #69e687 pseudobonds
+> color =sel #69e682 pseudobonds
+> color =sel #69e67f pseudobonds
+> color =sel #69e67d pseudobonds
+> color =sel #69e67e pseudobonds
+> color =sel #69e682 pseudobonds
+> color =sel #69e68c pseudobonds
+> color =sel #69e697 pseudobonds
+> color =sel #69e69e pseudobonds
+> color =sel #69e6b0 pseudobonds
+> color =sel #69e6bd pseudobonds
+> color =sel #69e6c2 pseudobonds
+> color =sel #69e6c8 pseudobonds
+> color =sel #69e6d0 pseudobonds
+> color =sel #69e6d6 pseudobonds
+> color =sel #69e6de pseudobonds
+> color =sel #69d0e6 pseudobonds
+> color =sel #69c7e6 pseudobonds
+> color =sel #69bee6 pseudobonds
+> color =sel #69b5e6 pseudobonds
+> color =sel #699ee6 pseudobonds
+> color =sel #6997e6 pseudobonds
+> color =sel #698ae6 pseudobonds
+> color =sel #6988e6 pseudobonds
+> color =sel #6985e6 pseudobonds
+> color =sel #6984e6 pseudobonds
+> color =sel #6983e6 pseudobonds
+> color =sel #6981e6 pseudobonds
+> color =sel #6980e6 pseudobonds
+> color =sel #697ee6 pseudobonds
+> color =sel #697de6 pseudobonds
+> color =sel #697be6 pseudobonds
+> color =sel #6979e6 pseudobonds
+> color =sel #6977e6 pseudobonds
+> color =sel #6976e6 pseudobonds
+> color =sel #6975e6 pseudobonds
+> color =sel #6974e6 pseudobonds
+> color =sel #6972e6 pseudobonds
+> color =sel #6971e6 pseudobonds
+> color =sel #6970e6 pseudobonds
+> color =sel #696fe6 pseudobonds
+> color =sel #696ae6 pseudobonds
+> color =sel #6c69e6 pseudobonds
+> color =sel #7969e6 pseudobonds
+> color =sel #8669e6 pseudobonds
+> color =sel #8a69e6 pseudobonds
+> color =sel #9669e6 pseudobonds
+> color =sel #9969e6 pseudobonds
+> color =sel #a469e6 pseudobonds
+> color =sel #a769e6 pseudobonds
+> color =sel #aa69e6 pseudobonds
+> color =sel #ac69e6 pseudobonds
+> color =sel #af69e6 pseudobonds
+> color =sel #b369e6 pseudobonds
+> color =sel #b669e6 pseudobonds
+> color =sel #b969e6 pseudobonds
+> color =sel #ba69e6 pseudobonds
+> color =sel #bc69e6 pseudobonds
+> color =sel #bd69e6 pseudobonds
+> color =sel #c069e6 pseudobonds
+> color =sel #c269e6 pseudobonds
+> color =sel #c369e6 pseudobonds
+> color =sel #c469e6 pseudobonds
+> color =sel #c969e6 pseudobonds
+> color =sel #cc69e6 pseudobonds
+> color =sel #cf69e6 pseudobonds
+> color =sel #d269e6 pseudobonds
+> color =sel #d469e6 pseudobonds
+> color =sel #da69e6 pseudobonds
+> color =sel #db69e6 pseudobonds
+> color =sel #dd69e6 pseudobonds
+> color =sel #e069e6 pseudobonds
+> color =sel #e169e6 pseudobonds
+> color =sel #e369e6 pseudobonds
+> color =sel #e469e6 pseudobonds
+> color =sel #e369e6 pseudobonds
+> color =sel #e269e6 pseudobonds
+> color =sel #de69e6 pseudobonds
+> color =sel #dd69e6 pseudobonds
+> color =sel #d969e6 pseudobonds
+> color =sel #d669e6 pseudobonds
+> color =sel #d469e6 pseudobonds
+> color =sel #d369e6 pseudobonds
+> color =sel #c669e6 pseudobonds
+> color =sel #c469e6 pseudobonds
+> color =sel #b969e6 pseudobonds
+> color =sel #b169e6 pseudobonds
+> color =sel #b069e6 pseudobonds
+> color =sel #ae69e6 pseudobonds
+> color =sel #ad69e6 pseudobonds
+> color =sel #ab69e6 pseudobonds
+> color =sel #a769e6 pseudobonds
+> color =sel #9869e6 pseudobonds
+> color =sel #9269e6 pseudobonds
+> color =sel #8269e6 pseudobonds
+> color =sel #7e69e6 pseudobonds
+> color =sel #7869e6 pseudobonds
+> color =sel #7769e6 pseudobonds
+> color =sel #7469e6 pseudobonds
+> color =sel #7269e6 pseudobonds
+> color =sel #7069e6 pseudobonds
+> color =sel #6c69e6 pseudobonds
+> color =sel #6b69e6 pseudobonds
+> color =sel #6a69e6 pseudobonds
+> color =sel #696ae6 pseudobonds
+> color =sel #696be6 pseudobonds
+> color =sel #696ce6 pseudobonds
+> color =sel #696be6 pseudobonds
+> color =sel #696ae6 pseudobonds
+> color =sel #6969e6 pseudobonds
+> color =sel #6a69e6 pseudobonds
+> color =sel #6b69e6 pseudobonds
+> color =sel #6c69e6 pseudobonds
+> color =sel #6d69e6 pseudobonds
+> color =sel #6e69e6 pseudobonds
+> color =sel #7069e6 pseudobonds
+> color =sel #7169e6 pseudobonds
+> color =sel #7269e6 pseudobonds
+> color =sel #7569e6 pseudobonds
+> color =sel #7769e6 pseudobonds
+> color =sel #7b69e6 pseudobonds
+> color =sel #8669e6 pseudobonds
+> color =sel #9269e6 pseudobonds
+> color =sel #9569e6 pseudobonds
+> color =sel #9669e6 pseudobonds
+> color =sel #9769e6 pseudobonds
+> color =sel #ff40ff pseudobonds
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 6 items
+> setattr =sel p halfbond false
+Assigning halfbond attribute to 6 items
+> select clear
+> color =sel #ff9300 pseudobonds
+> color =sel #ff40ff pseudobonds
+> hide sel
+> ui tool show "Selection Inspector"
+> color =sel #ff40ff pseudobonds
+> select clear
+> select /D:4@FE
+atom, 1 residue, 1 model selected
+> view sel
+> cofr sel
+> select clear
+> select /A:161@CD2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 15 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select /E:2@O
+atom, 1 residue, 1 model selected
+> select add /S:263@O
+atoms, 2 residues, 1 model selected
+> style sel ball
+Changed 2 atom styles
+> select clear
+> help help:user
+> surface cap true
+> select /A:120
+atoms, 3 bonds, 1 residue, 1 model selected
+> select add /A:121
+atoms, 8 bonds, 2 residues, 1 model selected
+> select add /A:122
+atoms, 11 bonds, 3 residues, 1 model selected
+> select add /A:123
+atoms, 26 bonds, 4 residues, 1 model selected
+> select subtract /A:123
+atoms, 11 bonds, 3 residues, 1 model selected
+> select add /A:141
+atoms, 18 bonds, 4 residues, 1 model selected
+> select subtract /A:141
+atoms, 11 bonds, 3 residues, 1 model selected
+> transparency sel 0
+> show sel surfaces
+> hide sel surfaces
+> select clear
+> show surfaces
+> hide surfaces
+> surface cap true
+> surface cap true offset 0.1
+> surface cap true offset 0.1 mesh false
+> toolshed show
+> select /A:163
+atoms, 10 bonds, 1 residue, 1 model selected
+> select /A:163
+atoms, 10 bonds, 1 residue, 1 model selected
+> select clear
+> show #1.2 target m
+[Repeated 2 time(s)]
+> view #1.2 clip false
+No displayed objects specified.
+> select add #1.3
+atoms, 198 residues, 3 models selected
+> select subtract #1.3
+model selected
+> select add #1.4
+atoms, 198 residues, 3 models selected
+> select subtract #1.4
+model selected
+> select add #1.4
+atoms, 198 residues, 3 models selected
+> select subtract #1.4
+model selected
+> select add #1.3
+atoms, 198 residues, 3 models selected
+> select subtract #1.3
+model selected
+> select add #1.4
+atoms, 198 residues, 3 models selected
+> select subtract #1.4
+model selected
+> select add #1.4.1
+model selected
+> select subtract #1.4.1
+Nothing selected
+> select add #1.4.2
+model selected
+> select subtract #1.4.2
+Nothing selected
+> select add #1.3.1
+model selected
+> select add #1.3.2
+models selected
+> select subtract #1.3.2
+model selected
+> select add #1.3.2
+models selected
+> select subtract #1.3.1
+model selected
+> select subtract #1.3.2
+Nothing selected
+> select add #1.3
+atoms, 198 residues, 3 models selected
+> select subtract #1.3
+model selected
+> select add #1.3
+atoms, 198 residues, 3 models selected
+> select subtract #1.3
+model selected
+> select add #1.3
+atoms, 198 residues, 3 models selected
+> hide #1.3.1 models
+> show #1.3.1 models
+> select subtract #1.3.1
+atoms, 198 residues, 3 models selected
+> select add #1.3.1
+atoms, 198 residues, 4 models selected
+> select subtract #1.3
+model selected
+> select add #1.4
+atoms, 198 residues, 3 models selected
+> select subtract #1.4
+model selected
+> select add #1.4
+atoms, 198 residues, 3 models selected
+> select subtract #1.4
+model selected
+> hide #!1.4 target m
+> hide #!1.3 models
+> show #1.3 models
+> select add #1.3
+atoms, 198 residues, 1 model selected
+> select subtract #1.3
+model selected
+> select add #1.3
+atoms, 198 residues, 1 model selected
+> select subtract #1.3
+model selected
+> select add #1.3
+atoms, 198 residues, 1 model selected
+> view #1.3 clip false
+No displayed objects specified.
+> select clear
+> surface cap true offset 0.2 mesh false
+> select surface cap
+Expected an objects specifier or a keyword
+> show surfaces cap
+Expected ',' or a keyword
+> show surfaces
+> hide surfaces
+> select clear
+> save /Users/sir_mr_dog/Desktop/image4.png supersample 3
+> toolshed show
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 Active site.cxs"
+> help help:user
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 active site
+> image.jpg" width 1142 height 765 supersample 3
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 active site
+> image_transparent.jpg" width 1142 height 765 supersample 3
+> transparentBackground true
+The JPEG file format does not support transparency, use PNG or TIFF instead.
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> toolshed show
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 active site
+> image.png" width 1142 height 765 supersample 3 transparentBackground true
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 Active site.cxs"
+——— End of log from Fri Apr 18 13:15:54 2025 ———
+opened ChimeraX session
+> open 7kks
+Summary of feedback from opening 7kks fetched from pdb
+---
+warnings | Atom D1 is not in the residue template for MET /A:0
+Atom D is not in the residue template for LYS /A:1
+Atom D is not in the residue template for HIS /A:2
+Atom D is not in the residue template for SER /A:3
+Atom D is not in the residue template for LEU /A:4
+Atom DA is not in the residue template for PRO /A:5
+Atom D is not in the residue template for ASP /A:6
+Atom D is not in the residue template for LEU /A:7
+Atom DA is not in the residue template for PRO /A:8
+Too many hydrogens missing from residue template(s) to warn about
+kks title:
+Neutron structure of Oxidized Human MnSOD [more info...]
+Chain information for 7kks #2
+---
+Chain | Description | UniProt
+A B | Superoxide dismutase [Mn], mitochondrial | SODM_HUMAN 1-198
+Non-standard residues in 7kks #2
+---
+MN3 — manganese (III) ion
+kks mmCIF Assemblies
+---
+| author_defined_assembly
+> ui tool show Matchmaker
+> matchmaker #!2 to #1
+Computing secondary structure
+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 KMnO4_rinsed_refine_034.pdb, chain A (#1) with 7kks, chain B (#2),
+sequence alignment score = 1069.2
+RMSD between 197 pruned atom pairs is 0.321 angstroms; (across all 198 pairs:
+.393)
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select clear
+> select #2/B:161@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select add #2/B:143@NE2
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 17 bonds, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> select #2/B:73@ND2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 13 bonds, 1 residue, 1 model selected
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2/B:34
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #2/B:30
+atoms, 36 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> select #2/B:34@OH
+atom, 1 residue, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> select add #1
+atoms, 3252 bonds, 17 pseudobonds, 1099 residues, 4 models selected
+> select subtract #1
+atom, 1 residue, 3 models selected
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #2/B:143@DE22
+atoms, 2 residues, 1 model selected
+> select clear
+> show #!1 models
+> hide #!1 models
+> select add #2/B:74@NE2
+atom, 4 pseudobonds, 1 residue, 2 models selected
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> ui tool show "Selection Inspector"
+> select up
+atoms, 3284 bonds, 266 residues, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select add #2/B:74@NE2
+atom, 2 pseudobonds, 1 residue, 2 models selected
+> select subtract #2/B:74@NE2
+pseudobonds, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr =sel p halfbond true
+Assigning halfbond attribute to 5 items
+> size =sel pseudobondRadius 0.065
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.055
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.045
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.035
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.025
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.035
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.045
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.055
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.065
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.075
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.085
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.095
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.105
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.115
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.125
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.135
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.145
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.165
+Changed 5 pseudobond radii
+> size =sel pseudobondRadius 0.155
+Changed 5 pseudobond radii
+> style sel stick segments 0
+Expected a keyword
+> help help:user
+> style sel stick dashes 0
+Changed 0 atom styles, 1 pseudobond dash
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide sel
+> select clear
+> select #2/B:122
+atoms, 6 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select clear
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> select add #2/B:160
+atoms, 40 bonds, 2 residues, 1 model selected
+> select add #2/B:162
+atoms, 54 bonds, 3 residues, 1 model selected
+> select add #2/B:163
+atoms, 71 bonds, 4 residues, 1 model selected
+> select clear
+> select #2/B:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select add #2/B:161
+atoms, 39 bonds, 2 residues, 1 model selected
+> select subtract #2/B:161
+atoms, 14 bonds, 1 residue, 1 model selected
+> select add #2/B:161
+atoms, 39 bonds, 2 residues, 1 model selected
+> select add #2/B:160
+atoms, 54 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #2/B:121
+atoms, 10 bonds, 1 residue, 1 model selected
+> hide sel
+> hide sel cartoons
+> select clear
+> select #2/B:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> select #2/B:161-150
+Nothing selected
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> show sel cartoons
+> select #2/B:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> select add #2/B:160
+atoms, 40 bonds, 2 residues, 1 model selected
+> select add #2/B:141
+atoms, 54 bonds, 3 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> style sel ball
+Changed 2 atom styles
+> select clear
+> select #2/B:336@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> style sel ball
+Changed 3 atom styles
+> select clear
+> color #2-3 #ff40ffff
+> color #2-3 #d369e6ff
+[Repeated 2 time(s)]
+> color #2-3 #d46ce6ff
+> color #2-3 #d46de6ff
+> color #2-3 #d470e6ff
+> color #2-3 #d471e6ff
+[Repeated 1 time(s)]
+> color #2-3 #d572e6ff
+[Repeated 1 time(s)]
+> color #2-3 #d573e6ff
+> color #2-3 #d67be6ff
+> color #2-3 #d67ce6ff
+> color #2-3 #d67ee6ff
+[Repeated 1 time(s)]
+> color #2-3 #d77fe6ff
+[Repeated 3 time(s)]
+> color #2-3 #d67ee6ff
+[Repeated 1 time(s)]
+> color #2-3 #d67de6ff
+[Repeated 1 time(s)]
+> color #2-3 #d67ce6ff
+[Repeated 1 time(s)]
+> color #2-3 #d67be6ff
+[Repeated 1 time(s)]
+> color #2-3 #d67ae6ff
+[Repeated 3 time(s)]
+> color #2-3 #d679e6ff
+[Repeated 2 time(s)]
+> color #2-3 #d678e6ff
+> color #2-3 #d578e6ff
+[Repeated 1 time(s)]
+> color #2-3 #d678e6ff
+> color #2-3 #d678e7ff
+> color #2-3 #d879e9ff
+> color #2-3 #d97aeaff
+> color #2-3 #da7aebff
+[Repeated 1 time(s)]
+> color #2-3 #db7becff
+[Repeated 1 time(s)]
+> color #2-3 #dc7bedff
+> color #2-3 #dd7ceeff
+[Repeated 1 time(s)]
+> color #2-3 #de7cefff
+> color #2-3 #df7df0ff
+> color #2-3 #df7df1ff
+> color #2-3 #e07df1ff
+> color #2-3 #e07ef2ff
+[Repeated 2 time(s)]
+> color #2-3 #e07df1ff
+> color #2-3 #df7df0ff
+> color #2-3 #de7cefff
+[Repeated 1 time(s)]
+> color #2-3 #de7df0ff
+> color #2-3 #df7df0ff
+> color #2-3 #e07ef2ff
+> color #2-3 #e17ef3ff
+> color #2-3 #e37ff5ff
+> color #2-3 #e580f6ff
+> color #2-3 #e580f7ff
+> color #2-3 #e581f7ff
+[Repeated 1 time(s)]
+> color #2-3 #e681f8ff
+> color #2-3 #e781f9ff
+> color #2-3 #e782f9ff
+> color #2-3 #e882faff
+[Repeated 4 time(s)]
+> color #2-3 #e987faff
+> color #2-3 #ea91faff
+> color #2-3 #eda4faff
+> color #2-3 #eda8faff
+[Repeated 1 time(s)]
+> color #2-3 #eda7faff
+[Repeated 1 time(s)]
+> color #2-3 #eda6faff
+[Repeated 2 time(s)]
+> color #2-3 #eda5faff
+[Repeated 1 time(s)]
+> color #2-3 #eda4faff
+> color #2-3 #eda2faff
+> color #2-3 #eca1faff
+> color #2-3 #eb99faff
+> color #2-3 #eb96faff
+> color #2-3 #ea91faff
+> color #2-3 #ea90faff
+> color #2-3 #ea8ffaff
+> color #2-3 #ea8efaff
+[Repeated 2 time(s)]
+> color #2-3 #ea8dfaff
+> color #2-3 #e98cfaff
+> color #2-3 #e98bfaff
+> color #2-3 #e885faff
+> color #2-3 #e884faff
+[Repeated 1 time(s)]
+> color #2-3 #e885faff
+> color #2-3 #e987faff
+[Repeated 1 time(s)]
+> color #2-3 #e989faff
+[Repeated 1 time(s)]
+> color #2-3 #e98afaff
+> color #2-3 #e98bfaff
+[Repeated 3 time(s)]
+> color #2-3 #e98cfaff
+> color #2-3 #e98bf9ff
+> color #2-3 #e287f2ff
+> color #2-3 #d37ee2ff
+> color #2-3 #cc7adaff
+> color #2-3 #c878d6ff
+> color #2-3 #c375d1ff
+> color #2-3 #bf72ccff
+> color #2-3 #b46cc1ff
+> color #2-3 #b26bbfff
+> color #2-3 #ae68bbff
+> color #2-3 #ae68baff
+[Repeated 1 time(s)]
+> color #2-3 #ae68bbff
+> color #2-3 #af69bbff
+> color #2-3 #b069bcff
+> color #2-3 #b16abeff
+> color #2-3 #bc70c9ff
+> color #2-3 #c475d2ff
+> color #2-3 #da83eaff
+> color #2-3 #df86efff
+> color #2-3 #e78af7ff
+> color #2-3 #ea8cfbff
+> color #2-3 #ee8fffff
+> color #2-3 byhetero
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active stie.cxs"
+——— End of log from Fri Apr 18 13:46:35 2025 ———
+opened ChimeraX session
+> view name active-site
+> show #!2 cartoons
+> sym #2 assembly 1
+Made 2 copies for 7kks assembly 1
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> ui tool show Matchmaker
+> matchmaker #!4.1 to #2 bring #!4.2
+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 7kks, chain B (#2) with 7kks, chain B (#4.1), sequence alignment
+score = 1085.2
+RMSD between 199 pruned atom pairs is 0.000 angstroms; (across all 199 pairs:
+.000)
+> hide #!4.1 models
+> show #!4.1 models
+> hide #!4.2 models
+> show #!4.2 models
+> hide #!4.1 models
+> close #4.1
+> select #4.2/B:166
+atoms, 20 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4.2/B:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #4.2/B:166@CZ
+atom, 1 residue, 1 model selected
+> select add #4.2/B:162@CD
+atoms, 2 residues, 1 model selected
+> select add #2/B:163@ND1
+atoms, 1 bond, 3 residues, 2 models selected
+> select up
+atoms, 1 bond, 4 residues, 2 models selected
+> select up
+atoms, 67 bonds, 4 residues, 2 models selected
+> ui tool show H-Bonds
+> hbonds sel color #ff40ff dashes 6 restrict both intraModel false reveal true
+> retainCurrent true
+hydrogen bonds found
+> select #4.2/B:120
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #4.2/B:119
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #4.2/B:120
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #4.2/B:121
+atoms, 16 bonds, 2 residues, 1 model selected
+> select add #4.2/B:119
+atoms, 32 bonds, 3 residues, 1 model selected
+> show sel atoms
+> hide sel atoms
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> color sel #ffccccff
+> color sel #ffc3c4ff
+> color sel #ffb9baff
+> color sel #ffacaeff
+> color sel #ff898bff
+> color sel #ff8285ff
+> color sel #ff7e80ff
+> color sel #ff7072ff
+> color sel #ff6e70ff
+> color sel #ff6d6fff
+> color sel #ff6c6fff
+> color sel #ff696cff
+> color sel #ff696bff
+> color sel #ff676aff
+> color sel #ff6769ff
+> color sel #ff6668ff
+> color sel #ff5e61ff
+> color sel #ff4f52ff
+> color sel #ff4b4eff
+> color sel #ff484bff
+> color sel #ff3e41ff
+[Repeated 1 time(s)]
+> color sel #ff3d41ff
+> color sel #ff393dff
+> color sel #ff373bff
+> color sel #ff3639ff
+> color sel #ff3438ff
+> color sel #ff3336ff
+> color sel #ff3135ff
+> color sel #ff2d30ff
+> color sel #ff2c30ff
+> color sel #ff2c2fff
+> color sel #ff2b2fff
+[Repeated 1 time(s)]
+> color sel #ff2becff
+> color sel #d42bffff
+> color sel #d32bffff
+> color sel #d02bffff
+> color sel #cd2bffff
+> color sel #ca2bffff
+> color sel #ba2bffff
+> color sel #b62bffff
+> color sel #b32bffff
+> color sel #b62bffff
+> color sel #b82bffff
+> color sel #c02bffff
+> color sel #c22bffff
+> color sel #c52bffff
+> color sel #c72bffff
+> color sel #ca2bffff
+> color sel #d72bffff
+> color sel #da2bffff
+> color sel #de2bffff
+> color sel #e12bffff
+> color sel #ed2bffff
+> color sel #f92bffff
+> color sel #fb2bffff
+> color sel #fd2bffff
+> color sel #ff2bffff
+> color sel #ff2bf3ff
+> color sel #ff2bf0ff
+> color sel #ff2bedff
+> color sel #ff2be0ff
+> color sel #ff2bdeff
+> color sel #ff2bdcff
+> color sel #ff2bd4ff
+> color sel #ff2bd2ff
+> color sel #ff2bd1ff
+[Repeated 1 time(s)]
+> color sel #ff2bd3ff
+> color sel #ff2bd5ff
+> color sel #ff2bd6ff
+> color sel #ff2bddff
+> color sel #ff2bdfff
+> color sel #ff2be6ff
+> color sel #ff2beeff
+> color sel #ff2bf1ff
+> color sel #ff2bf8ff
+> color sel #fa2bffff
+> color sel #f62bffff
+> color sel #f32bffff
+> color sel #ef2bffff
+> color sel #ec2bffff
+> color sel #e92bffff
+> color sel #e72bffff
+> color sel #e32bffff
+> color sel #e12bffff
+> color sel #df2bffff
+[Repeated 1 time(s)]
+> color sel #cb27e8ff
+[Repeated 1 time(s)]
+> color sel #ca27e7ff
+> color sel #c827e5ff
+> color sel #c626e2ff
+> color sel #c125ddff
+> color sel #bf25daff
+> color sel #be25d9ff
+[Repeated 1 time(s)]
+> color sel #bb16d9ff
+[Repeated 1 time(s)]
+> color sel #bb15d9ff
+> color sel #bb13d9ff
+> color sel #b908d9ff
+> color sel #b905d9ff
+> color sel #b800d9ff
+> color sel #b700d9ff
+[Repeated 1 time(s)]
+> color sel #ba00d9ff
+> color sel #d100d9ff
+> color sel #d900d9ff
+> color sel #d900cfff
+> color sel #d900caff
+> color sel #d900c7ff
+> color sel #d900aaff
+> color sel #d9009bff
+> color sel #d90096ff
+> color sel #d90095ff
+> color sel #d90097ff
+> color sel #d900a0ff
+> color sel #d900a2ff
+> color sel #d900a6ff
+> color sel #d900b9ff
+> color sel #d900bdff
+> color sel #d900bfff
+> color sel #d900c4ff
+> color sel #d900c8ff
+> color sel #d900ccff
+> color sel #d900d1ff
+> color sel #d900d6ff
+> color sel #d900d8ff
+> color sel #d500d9ff
+> color sel #d300d9ff
+> color sel #d100d9ff
+> color sel #cf00d9ff
+> color sel #cd00d9ff
+> color sel #c800d9ff
+> color sel #c700d9ff
+> color sel #c800d9ff
+> color sel #d900d1ff
+> color sel #d900cdff
+> color sel #d900bcff
+> color sel #d900a8ff
+> color sel #d9009aff
+> color sel #d90097ff
+> color sel #d9008fff
+> color sel #d9008cff
+> color sel #d90088ff
+> color sel #d90086ff
+> color sel #d90083ff
+[Repeated 1 time(s)]
+> color sel #d90085ff
+> color sel #d90089ff
+> color sel #d9008eff
+> color sel #d90091ff
+> color sel #d900a1ff
+> color sel #d900a9ff
+> color sel #d900abff
+> color sel #d900aeff
+> color sel #d90db0ff
+> color sel #d90eb1ff
+> color sel #d91bb3ff
+> color sel #d922b4ff
+> color sel #d924b5ff
+> color sel #d926b5ff
+> color sel #d929b6ff
+> color sel #d92fb7ff
+> color sel #d930b7ff
+[Repeated 1 time(s)]
+> color sel #d932b8ff
+> color sel #d935b8ff
+> color sel #d93cbaff
+[Repeated 1 time(s)]
+> color sel #d93dbaff
+[Repeated 1 time(s)]
+> color sel #d93ebaff
+> color sel #d93fbaff
+> color sel #d943bbff
+> color sel #d945bcff
+> color sel #d948bcff
+> color sel #d949bcff
+[Repeated 6 time(s)]
+> color sel #d948bcff
+> color sel #d947bcff
+> color sel #d945bbff
+> color sel #d941bbff
+> color sel #d922b5ff
+> color sel #d900aeff
+[Repeated 1 time(s)]
+> color sel #da00afff
+> color sel #f700c6ff
+> color sel #ff00ccff
+> color sel #fe00ccff
+> color sel #dd00b1ff
+> color sel #c900a1ff
+> color sel #b80093ff
+> color sel #b60092ff
+> color sel #b1008eff
+> color sel #b0008dff
+[Repeated 1 time(s)]
+> color sel #af008cff
+> color sel #a80086ff
+> color sel #a40084ff
+> color sel #a40083ff
+[Repeated 2 time(s)]
+> color sel #a50084ff
+> color sel #a90087ff
+> color sel #ae008bff
+> color sel #bb0096ff
+> color sel #d500aaff
+> color sel #d900aeff
+> color sel #e600b8ff
+> color sel #e600b9ff
+[Repeated 1 time(s)]
+> color sel #e600b8ff
+> color sel #e500b8ff
+> color sel #e500b7ff
+> color sel #e400b7ff
+[Repeated 1 time(s)]
+> select clear
+> select #2/B:325@O
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> hide sel
+> select clear
+> select #2/B:336@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> select clear
+> select #2/B:34@CZ
+atom, 1 residue, 1 model selected
+> select #2/B:143@DE22
+atom, 1 residue, 1 model selected
+> select #2/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #2/B:143@DE22
+atoms, 2 residues, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #ff40ff dashes 6 restrict both reveal true retainCurrent
+> true
+hydrogen bonds found
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> style sel sphere
+Changed 1 atom style
+> style sel ball
+Changed 1 atom style
+> style sel stick
+Changed 1 atom style
+> style sel sphere
+Changed 1 atom style
+> select clear
+> select #2/B:26@CD2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:123@CD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select #2/B:74@CE1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> show sel atoms
+> select clear
+> style #!2#!4.2 ball
+Changed 13182 atom styles
+> style #!2#!4.2 stick
+Changed 13182 atom styles
+> style #!2#!4.2 ball
+Changed 13182 atom styles
+> style #!2#!4.2 stick
+Changed 13182 atom styles
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> style sel sphere
+Changed 1 atom style
+> select clear
+> select #2/B:336@O
+atom, 1 residue, 1 model selected
+> select add #2/B:327@O
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 3 bonds, 2 residues, 1 model selected
+> style sel ball
+Changed 5 atom styles
+> select clear
+> color #4.2 #a262aeff
+> color #4.2 #ee8fffff
+> color #4.2 #a966b6ff
+> color #4.2 #a43fb6ff
+> color #4.2 #a12fb6ff
+> color #4.2 #8f2aa1ff
+> color #4.2 #8b11a1ff
+> color #4.2 #9031a1ff
+> color #4.2 #b73eccff
+> color #4.2 #892f99ff
+> select add #4.2
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 2 models selected
+> color (#!4.2 & sel) byhetero
+> select subtract #4.2
+Nothing selected
+> select add #3
+pseudobonds, 1 model selected
+> color #3 #ff40ffff models
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> color sel deep pink
+> select clear
+> view name active-site 2
+Expected fewer arguments
+> view name active-site-2
+> lighting soft
+> lighting simple
+> lighting full
+> lighting flat
+> volume projectionMode rays
+No volumes specified
+> lighting soft
+> lighting simple
+> lighting soft
+[Repeated 1 time(s)]
+> lighting full
+> lighting shadows false
+> toolshed show
+> ui autostart true "Side View"
+> help help:user
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_2.tif" width 1252 height 858 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_2_3xss.tif" width 1252 height 858 supersample 3
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_2_2xss.tif" width 1252 height 858 supersample 2
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_2_1xss.tif" width 1252 height 858 supersample 1
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_2_highres.tif" width 1576 height 1080 supersample 4
+> ui mousemode right label
+> label #2/B:26
+> label #2/B:201
+> label #2/B:163
+> label #4.2/B:162
+> label #4.2/B:166
+> label #2/B:161
+> label #2/B:143
+> label #2/B:123
+> label #2/B:73
+> label #2/B:34
+> label #2/B:327
+> label #2/B:336
+> label #2/B:74
+> label #2/B:159
+> ui mousemode right "move label"
+> help help:user
+> select clear
+[Repeated 3 time(s)]
+> ui tool show "Selection Inspector"
+> select clear
+[Repeated 2 time(s)]
+> view #2.3 clip false
+> view active-site-2
+[Repeated 1 time(s)]
+> select add #2.3
+model selected
+> ui tool show "Selection Inspector"
+> select subtract #2.3
+Nothing selected
+> select add #2.3
+model selected
+No visible atoms selected
+> select clear
+> select #2/B:336@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text "WAT 2"
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel text "WAT 1"
+> label sel text WAT1
+> select #2/B:336@O
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text WAT2
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> label sel atoms text Mn
+> label sel text Mn
+> ui mousemode right label
+> ui mousemode right "move label"
+> select clear
+> ui mousemode right label
+> label #2/B:30
+> ui mousemode right "move label"
+> ui mousemode right label
+> label #2/B:26
+> label #2/B:159
+> ui mousemode right "move label"
+> ui mousemode right "clip rotate"
+> ui mousemode right clip
+> ui mousemode right "clip rotate"
+[Repeated 2 time(s)]
+> view active-site-2
+[Repeated 1 time(s)]
+> ui mousemode right "move label"
+> lighting shadows true
+> lighting shadows false
+> lighting shadows true
+> lighting shadows false
+> view active-site-2
+> select #2/B:67
+atoms, 12 bonds, 1 residue, 1 model selected
+> select add #2/B:68
+atoms, 18 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> label #2-4 attribute label_one_letter_code
+> label #2-4 text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
+> undo
+[Repeated 1 time(s)]
+> ~label sel residues
+> select add #2
+atoms, 6556 bonds, 16 pseudobonds, 525 residues, 4 models selected
+> select add #4
+atoms, 13112 bonds, 26 pseudobonds, 1050 residues, 8 models selected
+> ~label (#!2#!4.2 & sel) residues
+> ~label (#!2#!4.2 & sel) atoms
+> select clear
+> select add #2/B:30@ND1
+atom, 2 bonds, 1 residue, 2 models selected
+> select add #2/B:163@DB2
+atoms, 2 bonds, 2 residues, 2 models selected
+> select add #2/B:163@CE1
+atoms, 2 bonds, 2 residues, 2 models selected
+> select add #2/B:336@O
+atoms, 5 bonds, 3 residues, 2 models selected
+> select add #2/B:327@O
+atoms, 5 bonds, 4 residues, 2 models selected
+> select add #2/B:123@CZ2
+atoms, 6 bonds, 5 residues, 2 models selected
+> select add #2/B:143@CG
+atoms, 6 bonds, 6 residues, 2 models selected
+> select add #2/B:73@CB
+atoms, 6 bonds, 7 residues, 2 models selected
+> select up
+atoms, 6 bonds, 13 residues, 2 models selected
+> select up
+atoms, 197 bonds, 13 residues, 2 models selected
+> select up
+atoms, 198 bonds, 14 residues, 2 models selected
+> select up
+atoms, 215 bonds, 14 residues, 2 models selected
+> select add #2/B:201@MN
+atoms, 215 bonds, 15 residues, 2 models selected
+> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
+> select clear
+> select up
+atoms, 2 bonds, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select clear
+> select #2/B:336@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text "WAT 2"
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel text "WAT 2"
+> label sel text "WAT 1"
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> label sel text Mn
+> select clear
+> select #2/B:142
+atoms, 13 bonds, 1 residue, 1 model selected
+> select add #2/B:143
+atoms, 29 bonds, 2 residues, 1 model selected
+> select add #2/B:144
+atoms, 40 bonds, 3 residues, 1 model selected
+> help help:user
+> select clear
+> select #2/B:143
+atoms, 16 bonds, 1 residue, 1 model selected
+> select down
+atoms, 16 bonds, 1 residue, 1 model selected
+> select down
+atoms, 16 bonds, 1 residue, 1 model selected
+> select down
+atoms, 16 bonds, 1 residue, 1 model selected
+> select down
+atoms, 16 bonds, 1 residue, 1 model selected
+> select down
+atoms, 16 bonds, 1 residue, 1 model selected
+> select down
+atoms, 16 bonds, 1 residue, 1 model selected
+> select #2/B:142
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/B:144
+atoms, 11 bonds, 1 residue, 1 model selected
+> select add #2/B:142
+atoms, 24 bonds, 2 residues, 1 model selected
+> select add #2/B:143
+atoms, 40 bonds, 3 residues, 1 model selected
+> ui tool show "Color Actions"
+> color sel #ff40ffff target cspf
+> color sel #ff40fffc target cspf
+> color sel #ff40ffe8 target cspf
+> color sel #ff40ffdc target cspf
+> color sel #ff40ffda target cspf
+> color sel #ff40ffd9 target cspf
+> color sel #ff40ffd8 target cspf
+> color sel #ff40ffd7 target cspf
+> color sel #ff40ffd6 target cspf
+> color sel #ff40ffd3 target cspf
+> color sel #ff40ffd1 target cspf
+> color sel #ff40ffcf target cspf
+> color sel #ff40ffcd target cspf
+> color sel #ff40ffca target cspf
+> color sel #ff40ffb9 target cspf
+> color sel #ff40ffb8 target cspf
+> color sel #ff40ffae target cspf
+> color sel #ff40ffac target cspf
+> color sel #ff40ffa0 target cspf
+> color sel #ff40ff9e target cspf
+> color sel #ff40ff97 target cspf
+> color sel #ff40ff96 target cspf
+> color sel #ff40ff94 target cspf
+> color sel #ff40ff8c target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff8b target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff8a target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff89 target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff88 target cspf
+> color sel #ff40ff87 target cspf
+> color sel #ff40ff7c target cspf
+> color sel #ff40ff6f target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff6e target cspf
+> color sel #ff40ff6b target cspf
+> color sel #ff40ff6a target cspf
+> color sel #ff40ff5e target cspf
+> color sel #ff40ff59 target cspf
+> color sel #ff40ff58 target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff59 target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff6b target cspf
+> color sel #ff40ff6e target cspf
+> color sel #ff40ff71 target cspf
+> color sel #ff40ff87 target cspf
+> color sel #ff40ffa4 target cspf
+> color sel #ff40ffac target cspf
+> color sel #ff40ffaf target cspf
+> color sel #ff40ffbe target cspf
+> color sel #ff40ffc3 target cspf
+> color sel #ff40ffcb target cspf
+> color sel #ff40ffbb target cspf
+> color sel #ff40ff9a target cspf
+> color sel #ff40ff86 target cspf
+> color sel #ff40ff71 target cspf
+> color sel #ff40ff67 target cspf
+> color sel #ff40ff66 target cspf
+[Repeated 4 time(s)]
+> color sel #ff40ff67 target cspf
+> color sel #ff40ff69 target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff6a target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ff71 target cspf
+> color sel #ff40ff72 target cspf
+> color sel #ff40ff73 target cspf
+> color sel #ff40ff7d target cspf
+> color sel #ff40ff81 target cspf
+> color sel #ff40ff83 target cspf
+> color sel #ff40ff8a target cspf
+> color sel #ff40ff99 target cspf
+> color sel #ff40ff9b target cspf
+> color sel #ff40ff9c target cspf
+> color sel #ff40ffa5 target cspf
+> color sel #ff40ffa9 target cspf
+> color sel #ff40ffab target cspf
+> color sel #ff40ffb4 target cspf
+> color sel #ff40ffb5 target cspf
+> color sel #ff40ffb3 target cspf
+> color sel #ff40ffb0 target cspf
+[Repeated 1 time(s)]
+> color sel #ff40ffaf target cspf
+> color sel #ff40ffae target cspf
+> color sel #ff40ffab target cspf
+> color sel #ff40ffa5 target cspf
+> color sel #ff40ff9c target cspf
+> color sel #ff40ff98 target cspf
+> color sel #ff40ff93 target cspf
+> color sel #ff40ff75 target cspf
+[Repeated 2 time(s)]
+> color sel #ff40ff76 target cspf
+> color sel #ff40ff90 target cspf
+> color sel #ff40ffcc target cspf
+> color sel #ff40fff4 target cspf
+> color sel #ff40ffff target cspf
+> color sel #ffbdffff target cspf
+> color sel #f694ffff target cspf
+[Repeated 1 time(s)]
+> color sel #f694fffe target cspf
+> color sel #f694fff6 target cspf
+> color sel #f694fff3 target cspf
+> color sel #f694ffeb target cspf
+> color sel #f694ffde target cspf
+> color sel #f694ffd7 target cspf
+> color sel #f694ffcc target cspf
+> color sel #f694ffbe target cspf
+> color sel #f694ffb6 target cspf
+> color sel #f694ffb5 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ffb3 target cspf
+> color sel #f694ffb2 target cspf
+> color sel #f694ffb0 target cspf
+> color sel #f694ffab target cspf
+[Repeated 2 time(s)]
+> color sel #f694ffaa target cspf
+> color sel #f694ffa4 target cspf
+> color sel #f694ffa3 target cspf
+> color sel #f694ff93 target cspf
+> color sel #f694ff91 target cspf
+> color sel #f694ff8e target cspf
+> color sel #f694ff8c target cspf
+> color sel #f694ff88 target cspf
+> color sel #f694ff87 target cspf
+[Repeated 4 time(s)]
+> color sel #f694ff88 target cspf
+> color sel #f694ff89 target cspf
+[Repeated 3 time(s)]
+> color sel #f694ff8a target cspf
+> color sel #f694ff95 target cspf
+> color sel #f694ff9b target cspf
+> color sel #f694ffbc target cspf
+> color sel #f694ffc1 target cspf
+> color sel #f694ffc5 target cspf
+> color sel #f694ffd6 target cspf
+> color sel #f694ffd7 target cspf
+> color sel #f694ffd5 target cspf
+> color sel #f694ffc7 target cspf
+> color sel #f694ffbe target cspf
+> color sel #f694ffb8 target cspf
+> color sel #f694ff81 target cspf
+> color sel #f694ff7a target cspf
+> color sel #f694ff6d target cspf
+> color sel #f694ff6b target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff6a target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff62 target cspf
+> color sel #f694ff57 target cspf
+> color sel #f694ff45 target cspf
+> color sel #f694ff42 target cspf
+> color sel #f694ff41 target cspf
+[Repeated 3 time(s)]
+> color sel #f694ff42 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff44 target cspf
+> color sel #f694ff59 target cspf
+> color sel #f694ff60 target cspf
+> color sel #f694ff73 target cspf
+> color sel #f694ff74 target cspf
+> color sel #f694ff76 target cspf
+> color sel #f694ff77 target cspf
+> color sel #f694ff76 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff75 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff74 target cspf
+> color sel #f694ff73 target cspf
+> color sel #f694ff70 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff6a target cspf
+> color sel #f694ff5c target cspf
+> color sel #f694ff4e target cspf
+> color sel #f694ff4d target cspf
+[Repeated 2 time(s)]
+> color sel #f694ff4e target cspf
+> color sel #f694ff4f target cspf
+> color sel #f694ff52 target cspf
+> color sel #f694ff61 target cspf
+> color sel #f694ff72 target cspf
+> color sel #f694ff74 target cspf
+> color sel #f694ff75 target cspf
+> color sel #f694ff76 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff73 target cspf
+> color sel #f694ff72 target cspf
+> color sel #f694ff6c target cspf
+> color sel #f694ff6b target cspf
+> color sel #f694ff6a target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff69 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff66 target cspf
+> color sel #f694ff65 target cspf
+> color sel #f694ff62 target cspf
+> color sel #f694ff61 target cspf
+> color sel #f694ff60 target cspf
+> color sel #f694ff5f target cspf
+[Repeated 2 time(s)]
+> color sel #f694ff60 target cspf
+> color sel #f694ff65 target cspf
+> color sel #f694ff66 target cspf
+> color sel #f694ff6d target cspf
+> color sel #f694ff75 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff79 target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff7a target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff7b target cspf
+> color sel #f694ff7c target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff7a target cspf
+> color sel #f694ff6e target cspf
+> color sel #f694ff6c target cspf
+> color sel #f694ff67 target cspf
+> color sel #f694ff63 target cspf
+> color sel #f694ff60 target cspf
+> color sel #f694ff5d target cspf
+[Repeated 1 time(s)]
+> color sel #f694ff5f target cspf
+> color sel #f694ff60 target cspf
+> color sel #f694ff6e target cspf
+> color sel #f694ff6f target cspf
+> color sel #f694ff71 target cspf
+> color sel #f694ff78 target cspf
+> color sel #f694ff7a target cspf
+> color sel #f694ff7c target cspf
+[Repeated 3 time(s)]
+> color sel #f694ff7b target cspf
+> color sel #f694ff7a target cspf
+[Repeated 2 time(s)]
+> color sel #f694ff7b target cspf
+> color sel #f694ff7c target cspf
+> color sel #f694ff7d target cspf
+> color sel #f694ff80 target cspf
+> select clear
+> select #2/B:327@D2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select #2/B:327@D2
+atom, 1 residue, 1 model selected
+> select #2/B:159@OD1
+atom, 1 residue, 1 model selected
+> ui tool show H-Bonds
+> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true
+hydrogen bonds found
+> select clear
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> show sel atoms
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> show sel cartoons
+> hide sel cartoons
+> select #2/B:161@N
+atom, 1 residue, 1 model selected
+> select #2/B:161@D
+atom, 1 residue, 1 model selected
+> select add #2/B:161@N
+atoms, 1 residue, 1 model selected
+> show sel cartoons
+> hide sel cartoons
+> hide sel atoms
+> show sel cartoons
+> hide sel cartoons
+> show sel atoms
+> show sel cartoons
+> ribbon sel suppressBackboneDisplay false
+> hide sel cartoons
+> select #2/B:161@O
+atom, 1 residue, 1 model selected
+> select add #2/B:161@C
+atoms, 1 residue, 1 model selected
+> select add #2/B:161@CA
+atoms, 1 residue, 1 model selected
+> select add #2/B:161@DA
+atoms, 1 residue, 1 model selected
+> select subtract #2/B:161@CA
+atoms, 1 residue, 1 model selected
+> select add #2/B:161@CA
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> select clear
+> select #2/B:143
+atoms, 16 bonds, 1 residue, 1 model selected
+> ribbon sel suppressBackboneDisplay false
+> select #2/B:143@D
+atom, 1 residue, 1 model selected
+> select add #2/B:143@N
+atoms, 1 residue, 1 model selected
+> select subtract #2/B:143
+Nothing selected
+> select #2/B:143
+atoms, 16 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> select #2/B:143@C
+atom, 1 residue, 1 model selected
+> select #2/B:143@CA
+atom, 1 residue, 1 model selected
+> select add #2/B:143@D
+atoms, 1 residue, 1 model selected
+> select add #2/B:143@N
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> show sel atoms
+> select #2/B:143@D
+atom, 1 residue, 1 model selected
+> select add #2/B:143@N
+atoms, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel cartoons
+> hide sel atoms
+> select #2/B:143@C
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> show sel atoms
+> ui tool show "Selection Inspector"
+> color =sel #ee8ffffe bonds
+> color =sel #ee8fffdc bonds
+> color =sel #ee8fffd9 bonds
+> color =sel #ee8fffc5 bonds
+> color =sel #ee8fffc3 bonds
+> color =sel #ee8fffba bonds
+> color =sel #ee8fffad bonds
+> color =sel #ee8fffa7 bonds
+> color =sel #ee8fff93 bonds
+> color =sel #ee8fff92 bonds
+> color =sel #ee8fff91 bonds
+> color =sel #ee8fff90 bonds
+> color =sel #ee8fff91 bonds
+> color =sel #ee8fff92 bonds
+> color =sel #ee8fff91 bonds
+> color =sel #ee8fff8f bonds
+> color =sel #ee8fff8d bonds
+> color =sel #ee8fff8b bonds
+> color =sel #ee8fff87 bonds
+> color =sel #ee8fff84 bonds
+> color =sel #ee8fff82 bonds
+> color =sel #ee8fff81 bonds
+> color =sel #ee8fff80 bonds
+> color =sel #ee8fff7d bonds
+> color =sel #ee8fff4d bonds
+> color =sel #ee8fff00 bonds
+> select clear
+> ui tool show "Selection Inspector"
+> color =sel #ee8fff03 bonds
+> color =sel #ee8fff13 bonds
+> color =sel #ee8fff7a bonds
+> color =sel #ee8fff8a bonds
+> color =sel #ee8fff93 bonds
+> color =sel #ee8fffc2 bonds
+> color =sel #ee8fffcc bonds
+> color =sel #ee8fffdb bonds
+> color =sel #ee8fff bonds
+> color =sel #ee8eff bonds
+> color =sel #ee8dff bonds
+> color =sel #ee8bff bonds
+> color =sel #ee75ff bonds
+> color =sel #ee73ff bonds
+> color =sel #ee72ff bonds
+> color =sel #ee71ff bonds
+> color =sel #ee70ff bonds
+> color =sel #ee6dff bonds
+> color =sel #ee5dff bonds
+> color =sel #ee58ff bonds
+> color =sel #ee4dff bonds
+> color =sel #ee4aff bonds
+> color =sel #ee47ff bonds
+> color =sel #ee3eff bonds
+> color =sel #ee31ff bonds
+> color =sel #ee30ff bonds
+> color =sel #ee21ff bonds
+> color =sel #ee1eff bonds
+> color =sel #ee05ff bonds
+> color =sel #ee04ff bonds
+> color =sel #ee00ff bonds
+> color =sel #ee01ff bonds
+> color =sel #ee11ff bonds
+> color =sel #ee94ff bonds
+> color =sel #eeb6ff bonds
+> color =sel #eeeeff bonds
+> color =sel #eefeff bonds
+> color =sel #eeffff bonds
+> color =sel #eefffffe bonds
+> color =sel #eeffffe3 bonds
+> color =sel #eeffff30 bonds
+> color =sel #eeffff28 bonds
+> color =sel #eeffff1a bonds
+> color =sel #eeffff13 bonds
+> color =sel #eeffff15 bonds
+> color =sel #eeffff1d bonds
+> color =sel #eeffff29 bonds
+> color =sel #eeffff4a bonds
+> color =sel #eeffff8a bonds
+> color =sel #eeffff96 bonds
+> color =sel #eeffff9d bonds
+> color =sel #eeffffb7 bonds
+> color =sel #eeffffb9 bonds
+> color =sel #eeffffbd bonds
+> color =sel #eeffffc8 bonds
+> color =sel #eeffffc9 bonds
+> color =sel #eeffffca bonds
+> color =sel #eefffff2 bonds
+> color =sel #eefffff8 bonds
+> color =sel #eefffff9 bonds
+> color =sel #edfffff9 bonds
+> color =sel #dcfffff9 bonds
+> color =sel #8bfffff9 bonds
+> color =sel #86fffff9 bonds
+> color =sel #85fffff9 bonds
+> color =sel #7efffff9 bonds
+> color =sel #7afffff9 bonds
+> color =sel #66fffff9 bonds
+> color =sel #942192 bonds
+> setattr =sel b display false
+Assigning display attribute to 1 item
+> setattr =sel b display true
+Assigning display attribute to 1 item
+> setattr =sel b display false
+Assigning display attribute to 1 item
+> select clear
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> hide sel cartoons
+> show sel atoms
+> select #2/B:161@DA
+atom, 1 residue, 1 model selected
+> select add #2/B:161@C
+atoms, 1 residue, 1 model selected
+> select add #2/B:161@O
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> show sel cartoons
+> hide sel cartoons
+> ui tool show "Selection Inspector"
+> setattr =sel b display false
+Assigning display attribute to 1 item
+> show sel cartoons
+> select clear
+[Repeated 1 time(s)]
+> view active-site-2
+> select #2/B:161@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr sel r thin_rings true
+Assigning thin_rings attribute to 1 item
+> setattr sel r thin_rings false
+Assigning thin_rings attribute to 1 item
+> color sel #ee8fffff
+[Repeated 1 time(s)]
+> color sel #ee8ffffb
+> color sel #ee8ffff5
+> color sel #ee8fffee
+> color sel #ee8fffeb
+> color sel #ee8fffcc
+> color sel #ee8fffb9
+> color sel #ee8fffb0
+[Repeated 1 time(s)]
+> color sel #ee8fffaf
+> color sel #ee8fffae
+> color sel #ee8fffac
+[Repeated 2 time(s)]
+> color sel #ee8fffab
+[Repeated 1 time(s)]
+> color sel #ee8fffa9
+> color sel #ee8fffa2
+> color sel #ee8fff9a
+> color sel #ee8fff83
+[Repeated 4 time(s)]
+> color sel #ee8fff84
+> color sel #ee8fff86
+> color sel #ee8fff87
+> color sel #ee8fff88
+> color sel #ee8fff89
+> color sel #ee8fff8a
+> color sel #ee8fff92
+> color sel #ee8fff93
+> color sel #ee8fff9b
+> color sel #ee8fffa1
+> color sel #ee8fffa8
+[Repeated 1 time(s)]
+> color sel #ee8fffab
+> color sel #ee8fffac
+> color sel #ee8fffaf
+[Repeated 1 time(s)]
+> color sel #ee8fffb0
+[Repeated 1 time(s)]
+> color sel #ee8fffb7
+> color sel #ee8fffbc
+> color sel #ee8fffcc
+> color sel #ee8fffd1
+[Repeated 1 time(s)]
+> color sel #ee8fffd0
+> color sel #ee8fffcf
+> color sel #ee8fffc0
+> color sel #ee8fffbe
+> color sel #ee8fffb9
+> color sel #ee8fffae
+> color sel #ee8fffaa
+> color sel #ee8fffa9
+> color sel #ee8fffa7
+[Repeated 2 time(s)]
+> color sel #ee8fffa4
+> color sel #ee8fffa3
+[Repeated 1 time(s)]
+> color sel #ee8fffa2
+> color sel #ee8fff9f
+> color sel #ee8fff9e
+> color sel #ee8fff9b
+> color sel #ee8fff9a
+> color sel #ee8fff98
+> color sel #ee8fff90
+> color sel #ee8fff8f
+[Repeated 1 time(s)]
+> color sel #ee8fff90
+> color sel #ee8fff97
+> color sel #ee8fff98
+> color sel #ee8fff9a
+> color sel #ee8fffa4
+> color sel #ee8fffa6
+> color sel #ee8fffa8
+> color sel #ee8fffa9
+> color sel #ee8fffac
+[Repeated 1 time(s)]
+> color sel #ee8fffad
+> color sel #ee8fffae
+> color sel #ee8fffaf
+> color sel #ee8fffb0
+[Repeated 4 time(s)]
+> color sel #ee8fffaf
+[Repeated 1 time(s)]
+> color sel #ee8fffae
+[Repeated 2 time(s)]
+> color sel #ee8fffad
+> color sel #ee8fffac
+> color sel #ee8fff8c
+> color sel #ee8fff85
+> color sel #ee8fff83
+> color sel #ee8fff81
+[Repeated 1 time(s)]
+> color sel #ee8fff82
+> color sel #ee8fff86
+> color sel #ee8fff88
+> color sel #ee8fff91
+> color sel #ee8fff94
+> color sel #ee8fff95
+> color sel #ee8fffa0
+> color sel #ee8fffa4
+> color sel #ee8fffa5
+[Repeated 2 time(s)]
+> color sel #ee8fffa3
+> color sel #ee8fffa0
+> color sel #ee8fff90
+> color sel #ee8fff8d
+> color sel #ee8fff89
+> color sel #ee8fff88
+> color sel #ee8fff86
+> color sel #ee8fff85
+> color sel #ee8fff84
+[Repeated 1 time(s)]
+> color sel #ee8fff85
+> color sel #ee8fff86
+[Repeated 1 time(s)]
+> color sel #ee8fff87
+> color sel #ee8fff89
+> color sel #ee8fff8c
+> color sel #ee8fff8d
+> color sel #ee8fff8f
+> color sel #ee8fff90
+> color sel #ee8fff98
+> color sel #ee8fffbb
+> color sel #ee8fffc9
+> color sel #ee8fffe9
+> color sel #ee8ffffb
+> color sel #ee8fffff
+> color sel #ee8ffff5
+> color sel #ee8fffab
+> color sel #ee8fff78
+> color sel #ee8fff76
+> color sel #ee8fff75
+> color sel #ee8fff73
+[Repeated 1 time(s)]
+> color sel #ee8fff74
+[Repeated 1 time(s)]
+> color sel #ee8fff75
+> color sel #ee8fff76
+[Repeated 3 time(s)]
+> color sel #ee8fff77
+> color sel #ee8fff78
+> color sel #ee8fff79
+[Repeated 1 time(s)]
+> color sel #ee8fff7a
+> color sel #ee8fff7b
+> color sel #ee8fff7c
+> color sel #ee8fff7e
+> color sel #ee8fff81
+> color sel #ee8fff88
+> color sel #ee8fff91
+[Repeated 1 time(s)]
+> color sel #ee8fff95
+> color sel #ee8fffa8
+> color sel #ee8fffd7
+> color sel #ee8ffff6
+> color sel #ee8fffff
+[Repeated 1 time(s)]
+> color sel #ee8ffffd
+> color sel #ee8ffff6
+> color sel #ee8fffee
+> color sel #ee8fffd8
+> color sel #ee8fffd2
+> color sel #ee8fffd0
+> color sel #ee8fffcb
+> color sel #ee8fffc8
+> color sel #ee8fffc2
+> color sel #ee8fffb3
+> color sel #ee8fffb2
+> color sel #ee8fffb1
+> color sel #ee8fffab
+> color sel #ee8fffa4
+> color sel #ee8fffa3
+> color sel #ee8fff93
+> color sel #ee8fff8d
+[Repeated 2 time(s)]
+> color sel #ee8fff8c
+> color sel #ee8fff8d
+[Repeated 1 time(s)]
+> color sel #ee8fff8e
+[Repeated 2 time(s)]
+> color sel #ee8fff8f
+[Repeated 1 time(s)]
+> color sel #ee8fff92
+> color sel #ee8fff99
+> color sel #ee8fff9b
+> color sel #ee8fffb2
+> color sel #ee8fffec
+> color sel #ee8ffff3
+> color sel #ee8fffff
+> ui tool show "Color Actions"
+> color sel #ee8ffffe target aspf
+> color sel #ee8ffff9 target aspf
+> color sel #ee8fffd5 target aspf
+> color sel #ee8fffd1 target aspf
+> color sel #ee8fffce target aspf
+> color sel #ee8fffc3 target aspf
+> color sel #ee8fffc1 target aspf
+> color sel #ee8fffb7 target aspf
+> color sel #ee8fffb6 target aspf
+> color sel #ee8fffb5 target aspf
+> color sel #ee8fffb4 target aspf
+> color sel #ee8fffb3 target aspf
+> color sel #ee8fffb1 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffa8 target aspf
+> color sel #ee8fffa4 target aspf
+> color sel #ee8fff9e target aspf
+> color sel #ee8fff9d target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff9c target aspf
+[Repeated 4 time(s)]
+> color sel #ee8fff9d target aspf
+> color sel #ee8fff9e target aspf
+> color sel #ee8fffa4 target aspf
+> color sel #ee8fffc4 target aspf
+> color sel #ee8fffc8 target aspf
+> color sel #ee8fffe7 target aspf
+> color sel #ee8fffea target aspf
+> color sel #ee8ffffa target aspf
+> color sel #ee8fffff target aspf
+> color sel #ee8ffff1 target aspf
+> color sel #ee8fff8e target aspf
+> color sel #ee8fff84 target aspf
+> color sel #ee8fff79 target aspf
+> color sel #ee8fff67 target aspf
+> color sel #ee8fff66 target aspf
+> color sel #ee8fff64 target aspf
+> color sel #ee8fff63 target aspf
+> color sel #ee8fff56 target aspf
+> color sel #ee8fff54 target aspf
+> color sel #ee8fff52 target aspf
+> color sel #ee8fff4c target aspf
+> color sel #ee8fff49 target aspf
+> color sel #ee8fff39 target aspf
+> color sel #ee8fff29 target aspf
+> color sel #ee8fff28 target aspf
+> color sel #ee8fff26 target aspf
+> color sel #ee8fff23 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fff24 target aspf
+> color sel #ee8fff27 target aspf
+> color sel #ee8fff32 target aspf
+> color sel #ee8fff3f target aspf
+> color sel #ee8fff42 target aspf
+> color sel #ee8fff5d target aspf
+> color sel #ee8fff6c target aspf
+> color sel #ee8fff6f target aspf
+> color sel #ee8fff7d target aspf
+> color sel #ee8fff8a target aspf
+> color sel #ee8fffb1 target aspf
+> color sel #ee8fffb8 target aspf
+> color sel #ee8fffec target aspf
+> color sel #ee8ffff2 target aspf
+> color sel #ee8ffff7 target aspf
+> color sel #ee8fffff target aspf
+> color sel #ee8fffef target aspf
+> color sel #ee8fffd5 target aspf
+> color sel #ee8fff86 target aspf
+> color sel #ee8fff81 target aspf
+> color sel #ee8fff70 target aspf
+> color sel #ee8fff6e target aspf
+> color sel #ee8fff6d target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff6f target aspf
+> color sel #ee8fff70 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff79 target aspf
+> color sel #ee8fff7d target aspf
+> color sel #ee8fffbe target aspf
+> color sel #ee8fffc6 target aspf
+> color sel #ee8ffff5 target aspf
+> color sel #ee8ffffc target aspf
+> color sel #ee8ffffe target aspf
+> color sel #ee8fffff target aspf
+> color sel #ee8ffff4 target aspf
+> color sel #ee8fffeb target aspf
+> color sel #ee8fff83 target aspf
+> color sel #ee8fff6a target aspf
+> color sel #ee8fff4d target aspf
+> color sel #ee8fff48 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff47 target aspf
+> color sel #ee8fff48 target aspf
+> color sel #ee8fff49 target aspf
+> color sel #ee8fff4a target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff4b target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff4a target aspf
+> color sel #ee8fff49 target aspf
+> color sel #ee8fff47 target aspf
+> color sel #ee8fff49 target aspf
+> color sel #ee8fff4b target aspf
+> color sel #ee8fff56 target aspf
+> color sel #ee8fff67 target aspf
+> color sel #ee8fff6c target aspf
+> color sel #ee8fff74 target aspf
+[Repeated 4 time(s)]
+> color sel #ee8fff78 target aspf
+> color sel #ee8fff7e target aspf
+> color sel #ee8fff85 target aspf
+> color sel #ee8fff9b target aspf
+> color sel #ee8fff9c target aspf
+> color sel #ee8fff9b target aspf
+> color sel #ee8fff9a target aspf
+> color sel #ee8fff91 target aspf
+> color sel #ee8fff84 target aspf
+> color sel #ee8fff83 target aspf
+[Repeated 3 time(s)]
+> color sel #ee8fff82 target aspf
+> color sel #ee8fff80 target aspf
+> color sel byhetero target aspf
+> color sel #ee8fff80 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff86 target aspf
+> color sel #ee8fff87 target aspf
+> color sel #ee8fff8e target aspf
+> color sel #ee8fff8f target aspf
+> color sel #ee8fff91 target aspf
+> color sel #ee8fff97 target aspf
+> color sel #ee8fff99 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff9c target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff9f target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffa2 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffa7 target aspf
+> color sel #ee8fffa9 target aspf
+> color sel #ee8fffb0 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb3 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb4 target aspf
+> color sel #ee8fffb9 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffba target aspf
+> color sel #ee8fffbb target aspf
+> color sel #ee8fffbc target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffbd target aspf
+[Repeated 3 time(s)]
+> color sel #ee8fffbc target aspf
+> color sel #ee8fffbb target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffba target aspf
+> color sel #ee8fffb9 target aspf
+> color sel #ee8fffb8 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffb9 target aspf
+> color sel #ee8fffba target aspf
+> color sel #ee8fffbc target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffbd target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffbe target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffcd target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffcc target aspf
+> color sel #ee8fffcb target aspf
+> color sel #ee8fffc9 target aspf
+> color sel #ee8fffc7 target aspf
+> color sel #ee8fffc6 target aspf
+> color sel #ee8fffc5 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffc4 target aspf
+> color sel #ee8fffbe target aspf
+> color sel #ee8fffb6 target aspf
+> color sel #ee8fffb5 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb4 target aspf
+> color sel #ee8fffb0 target aspf
+> color sel #ee8fffaf target aspf
+> color sel #ee8fffae target aspf
+> color sel #ee8fffac target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffab target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffaa target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffa9 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffa8 target aspf
+[Repeated 4 time(s)]
+> color sel #ee8fffa7 target aspf
+[Repeated 5 time(s)]
+> color sel #ee8fffa6 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffa5 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffa4 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fff9f target aspf
+[Repeated 3 time(s)]
+> color sel #ee8fff9e target aspf
+> color sel #ee8fff9d target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fff9c target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fff9b target aspf
+> color sel #ee8fff9a target aspf
+> color sel #ee8fff98 target aspf
+> color sel #ee8fff97 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff99 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff9b target aspf
+> color sel #ee8fff9d target aspf
+> color sel #ee8fff9e target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff9d target aspf
+> color sel #ee8fff9c target aspf
+> color sel #ee8fff9a target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fff99 target aspf
+> color sel #ee8fff98 target aspf
+> color sel #ee8fff99 target aspf
+> color sel byhetero target aspf
+> color sel #ee8fff99 target aspf
+> color sel #ee8fff9f target aspf
+> color sel #ee8fffa5 target aspf
+> color sel #ee8fffa6 target aspf
+> color sel #ee8fffa8 target aspf
+> color sel #ee8fffa9 target aspf
+> color sel #ee8fffac target aspf
+[Repeated 5 time(s)]
+> color sel #ee8fffad target aspf
+> color sel #ee8fffb1 target aspf
+> color sel #ee8fffb2 target aspf
+> color sel #ee8fffbc target aspf
+> color sel #ee8fffc5 target aspf
+> color sel #ee8fffc8 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffc9 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffc8 target aspf
+> color sel #ee8fffc7 target aspf
+> color sel #ee8fffc6 target aspf
+> color sel #ee8fffc5 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffc4 target aspf
+[Repeated 3 time(s)]
+> color sel #ee8fffc5 target aspf
+> color sel #ee8fffc7 target aspf
+> color sel #ee8fffc8 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffc9 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffca target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffcb target aspf
+> color sel #ee8fffcc target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffcb target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffca target aspf
+> color sel #ee8fffc7 target aspf
+> color sel #ee8fffc4 target aspf
+> color sel #ee8fffc3 target aspf
+> color sel #ee8fffc2 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffc0 target aspf
+> color sel #ee8fffbc target aspf
+> color sel #ee8fffba target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb9 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb8 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb7 target aspf
+> color sel #ee8fffb6 target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffb5 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb6 target aspf
+[Repeated 1 time(s)]
+> color sel #ee8fffb9 target aspf
+> color sel #ee8fffbd target aspf
+> color sel #ee8fffbe target aspf
+> color sel #ee8fffc0 target aspf
+> color sel #ee8fffc1 target aspf
+[Repeated 5 time(s)]
+> color sel #ee8fffc0 target aspf
+> color sel #ee8fffbf target aspf
+[Repeated 2 time(s)]
+> color sel #ee8fffbe target aspf
+[Repeated 1 time(s)]
+> color sel byhetero target aspf
+> select #2/B:161@D
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select subtract #2/B:161
+Nothing selected
+> select #2/B:161@D
+atom, 1 residue, 1 model selected
+> hide sel cartoons
+> select add #2/B:161@D
+atom, 1 pseudobond, 1 residue, 2 models selected
+> select clear
+> select #2/B:161@D
+atom, 1 residue, 1 model selected
+> color sel #ee8fffbf target aspf
+> color sel #ee8fffc1 target aspf
+> color sel #ee8fffff target aspf
+> select #2/B:160
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #2/B:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2/B:161@CA
+atom, 1 residue, 1 model selected
+> select #2/B:161@D
+atom, 1 residue, 1 model selected
+> select #2/B:161@N
+atom, 1 residue, 1 model selected
+> color sel #ee8fffff target aspf
+> color sel #ee8fff00 target aspf
+> color sel #ee8fff0c target aspf
+> color sel #ee8ffffb target aspf
+> color sel #ee8fffff target aspf
+> show sel cartoons
+> select clear
+> select #2/B:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> color sel byhetero target aspf
+> select clear
+> select subtract #2.2
+Nothing selected
+> select add #2.3
+model selected
+> ui tool show "Selection Inspector"
+> select clear
+> view name active-site-3
+> view active-site
+> view active-site-2
+> view active-site-3
+> view name active-site-3
+> view active-site-3
+[Repeated 1 time(s)]
+> select #2/B:143
+atoms, 16 bonds, 1 residue, 1 model selected
+> select add #2/B:142
+atoms, 29 bonds, 2 residues, 1 model selected
+> select subtract #2/B:143
+atoms, 13 bonds, 1 residue, 1 model selected
+> select #2/B:143
+atoms, 16 bonds, 1 residue, 1 model selected
+> color sel #ee8ffffe target cspf
+> color sel #ee8ffff4 target cspf
+> color sel #ee8fffd4 target cspf
+> color sel #ee8fffd5 target cspf
+[Repeated 1 time(s)]
+> color sel #ee8fffd9 target cspf
+> color sel #ee8fffda target cspf
+> color sel #ee8fffff target cspf
+> select add #2/B:142
+atoms, 29 bonds, 2 residues, 1 model selected
+> color sel #ee8ffffe target cspf
+> color sel #ee8fffa6 target cspf
+> color sel #ee8fff9e target cspf
+> color sel #ee8fff97 target cspf
+[Repeated 1 time(s)]
+> color sel #ee8fff99 target cspf
+> color sel #ee8fff9a target cspf
+> color sel #ee8fffa8 target cspf
+> color sel #ee8fffff target cspf
+> select clear
+> select add #2/B:161@CZ3
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #2/B:161@D
+atom, 1 residue, 1 model selected
+> select #2/B:161@CB
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show sel atoms
+> hide sel cartoons
+> select #2/B:161@O
+atom, 1 residue, 1 model selected
+> select add #2/B:161@C
+atoms, 1 residue, 1 model selected
+> select add #2/B:161@DA
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select #2/B:180
+atoms, 18 bonds, 1 residue, 1 model selected
+> select #2/B:161@N
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> select #2/B:161@N
+atom, 1 residue, 1 model selected
+> select #2/B:161@CB
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> select subtract #2/B:161@D
+atoms, 24 bonds, 1 residue, 1 model selected
+> select subtract #2/B:161@N
+atoms, 23 bonds, 1 pseudobond, 1 residue, 2 models selected
+> color (#!2 & sel) #ee8fffff target cspf
+> color (#!2 & sel) #ee8fffed target cspf
+> color (#!2 & sel) #ee8fffe0 target cspf
+> color (#!2 & sel) #ee8fffc5 target cspf
+> color (#!2 & sel) #ee8fffc4 target cspf
+> color (#!2 & sel) #ee8fffc3 target cspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fffbf target cspf
+> color (#!2 & sel) #ee8fffb9 target cspf
+> color (#!2 & sel) #ee8fffb4 target cspf
+> color (#!2 & sel) #ee8fffac target cspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fffab target cspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fffac target cspf
+> color (#!2 & sel) #ee8fffab target cspf
+> color (#!2 & sel) #ee8fffa6 target cspf
+> color (#!2 & sel) #ee8fff7e target cspf
+> color (#!2 & sel) #ee8fff7c target cspf
+> color (#!2 & sel) #ee8fff76 target cspf
+> color (#!2 & sel) #ee8fff78 target cspf
+> color (#!2 & sel) #ee8fffa0 target cspf
+> color (#!2 & sel) #ee8fffb3 target cspf
+> color (#!2 & sel) #ee8fffcd target cspf
+> color (#!2 & sel) #ee8fffce target cspf
+> color (#!2 & sel) #ee8fffcf target cspf
+> color (#!2 & sel) #ee8fffd4 target cspf
+> color (#!2 & sel) #ee8fffff target cspf
+> color (#!2 & sel) #ee8fffff target aspf
+> color (#!2 & sel) #ee8fffc4 target aspf
+> color (#!2 & sel) #ee8fffc2 target aspf
+> color (#!2 & sel) #ee8fffbf target aspf
+> color (#!2 & sel) #ee8fffa8 target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fffa9 target aspf
+> color (#!2 & sel) #ee8fffaa target aspf
+> color (#!2 & sel) #ee8fffaf target aspf
+> color (#!2 & sel) #ee8fffc4 target aspf
+> color (#!2 & sel) #ee8fffc5 target aspf
+> color (#!2 & sel) #ee8fffd5 target aspf
+> color (#!2 & sel) #ee8fffda target aspf
+> color (#!2 & sel) #ee8fffde target aspf
+> color (#!2 & sel) #ee8fffe4 target aspf
+> color (#!2 & sel) #ee8ffff4 target aspf
+> color (#!2 & sel) #ee8ffff6 target aspf
+> color (#!2 & sel) #ee8ffffd target aspf
+> color (#!2 & sel) #ee8ffff8 target aspf
+> color (#!2 & sel) #ee8ffff0 target aspf
+> color (#!2 & sel) #ee8fffb0 target aspf
+> color (#!2 & sel) #ee8fffa8 target aspf
+> color (#!2 & sel) #ee8fff9a target aspf
+> color (#!2 & sel) #ee8fff99 target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff98 target aspf
+> color (#!2 & sel) #ee8fff7a target aspf
+> color (#!2 & sel) #ee8fff6e target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff6f target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff73 target aspf
+> color (#!2 & sel) #ee8fff74 target aspf
+> color (#!2 & sel) #ee8fff78 target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff79 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff7a target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff7b target aspf
+> color (#!2 & sel) #ee8fff7c target aspf
+> color (#!2 & sel) #ee8fff7d target aspf
+[Repeated 3 time(s)]
+> color (#!2 & sel) #ee8fff7e target aspf
+> color (#!2 & sel) #ee8fff80 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff8d target aspf
+> color (#!2 & sel) #ee8fff92 target aspf
+> color (#!2 & sel) #ee8fff96 target aspf
+> color (#!2 & sel) #ee8fff98 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff97 target aspf
+> color (#!2 & sel) #ee8fff96 target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff95 target aspf
+> color (#!2 & sel) #ee8fff94 target aspf
+> color (#!2 & sel) #ee8fff8d target aspf
+> color (#!2 & sel) #ee8fff85 target aspf
+> color (#!2 & sel) #ee8fff84 target aspf
+> color (#!2 & sel) #ee8fff7b target aspf
+> color (#!2 & sel) #ee8fff79 target aspf
+> color (#!2 & sel) #ee8fff7a target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff7d target aspf
+> color (#!2 & sel) #ee8fff7e target aspf
+> color (#!2 & sel) #ee8fff81 target aspf
+> color (#!2 & sel) #ee8fff82 target aspf
+> color sel byhetero target aspf
+> color (#!2 & sel) #ee8fff83 target aspf
+> color (#!2 & sel) #ee8fff9e target aspf
+> color (#!2 & sel) #ee8fffa0 target aspf
+> color (#!2 & sel) #ee8fffb4 target aspf
+> color (#!2 & sel) #ee8fffb7 target aspf
+> color (#!2 & sel) #ee8fffb9 target aspf
+> color (#!2 & sel) #ee8fffbb target aspf
+> color (#!2 & sel) #ee8fffc8 target aspf
+> color (#!2 & sel) #ee8fffcf target aspf
+> color (#!2 & sel) #ee8fffd0 target aspf
+> color (#!2 & sel) #ee8fffd2 target aspf
+> color (#!2 & sel) #ee8fffe7 target aspf
+> color (#!2 & sel) #ee8fffeb target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fffec target aspf
+> color (#!2 & sel) #ee8fffef target aspf
+> color (#!2 & sel) #ee8ffff0 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fffef target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fffee target aspf
+> color (#!2 & sel) #ee8fffed target aspf
+> color (#!2 & sel) #ee8fffeb target aspf
+> color (#!2 & sel) #ee8fffe4 target aspf
+> color (#!2 & sel) #ee8fffe1 target aspf
+> color (#!2 & sel) #ee8fffca target aspf
+> color (#!2 & sel) #ee8fffc4 target aspf
+> color (#!2 & sel) #ee8fffbf target aspf
+> color (#!2 & sel) #ee8fffba target aspf
+> color (#!2 & sel) #ee8fffb8 target aspf
+> color (#!2 & sel) #ee8fffac target aspf
+> color (#!2 & sel) #ee8fff91 target aspf
+> color (#!2 & sel) #ee8fff8d target aspf
+> color (#!2 & sel) #ee8fff8c target aspf
+> color (#!2 & sel) #ee8fff88 target aspf
+> color (#!2 & sel) #ee8fff65 target aspf
+> color (#!2 & sel) #ee8fff60 target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff61 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff62 target aspf
+> color (#!2 & sel) #ee8fff65 target aspf
+> color (#!2 & sel) #ee8fff66 target aspf
+> color (#!2 & sel) #ee8fff68 target aspf
+> color (#!2 & sel) #ee8fff6c target aspf
+> color (#!2 & sel) #ee8fff6d target aspf
+> color (#!2 & sel) #ee8fff6e target aspf
+> color (#!2 & sel) #ee8fff72 target aspf
+> color (#!2 & sel) #ee8fff76 target aspf
+> color (#!2 & sel) #ee8fff79 target aspf
+> color (#!2 & sel) #ee8fff7b target aspf
+> color (#!2 & sel) #ee8fff7c target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff7a target aspf
+> color (#!2 & sel) #ee8fff79 target aspf
+> color (#!2 & sel) #ee8fff6f target aspf
+> color (#!2 & sel) #ee8fff6d target aspf
+> color (#!2 & sel) #ee8fff67 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff66 target aspf
+[Repeated 2 time(s)]
+> color (#!2 & sel) #ee8fff65 target aspf
+> color (#!2 & sel) #ee8fff64 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff63 target aspf
+> color (#!2 & sel) #ee8fff68 target aspf
+> color (#!2 & sel) #ee8fff71 target aspf
+> color (#!2 & sel) #ee8fff73 target aspf
+[Repeated 1 time(s)]
+> color (#!2 & sel) #ee8fff75 target aspf
+> color (#!2 & sel) #ee8fff77 target aspf
+> color (#!2 & sel) #ee8fff78 target aspf
+> color (#!2 & sel) #ee8fff79 target aspf
+> color (#!2 & sel) #ee8fff80 target aspf
+> color sel byhetero target aspf
+> show sel cartoons
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> select add #2/B:336@O
+atoms, 2 residues, 1 model selected
+> select add #2/B:327@O
+atoms, 3 residues, 1 model selected
+> select up
+atoms, 3 bonds, 3 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6553 bonds, 16 pseudobonds, 522 residues, 3 models selected
+> style sel ball
+Changed 6585 atom styles
+> style sel stick
+Changed 6585 atom styles
+> style sel ball
+Changed 6585 atom styles
+> style sel stick
+Changed 6585 atom styles
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_3_highres.tif" width 1421 height 1080 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active stie.cxs"
+> select clear
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel bgColor whitw
+Invalid "bgColor" argument: Expected 'none' or a color
+> label sel bgColor white
+> select #2/B:143@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 16 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> label sel bgColor none
+> label sel height fixed
+> label sel defaultHeight
+Missing "defaultHeight" keyword's argument
+> label sel height defaultHeight
+Invalid "height" argument: Expected 'fixed' or a number
+> label sel height default
+Invalid "height" argument: Expected 'fixed' or a number
+> label sel height 0
+> label sel height 2
+> label sel height 1
+> label sel height 0.5
+> label sel height 0.6
+> label sel height 0.7
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel size 40
+> label sel size 42
+> label sel size 48
+> label sel size 30
+> label sel size 48
+> label sel height 0.5
+> label sel height 0.6
+> select clear
+> select #2/B:159@OD2
+atom, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel height 0.65
+> select clear
+> select #2/B:144
+atoms, 11 bonds, 1 residue, 1 model selected
+> color sel #ee8fff7f target cspf
+> color sel #ee8fff77 target cspf
+> color sel #ee8fff00 target cspf
+> color sel #ee8fff01 target cspf
+> color sel #ee8fff04 target cspf
+> color sel #ee8fffff target cspf
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_3_highres.tif" width 1421 height 1080 supersample 4
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active stie.cxs"
+> help help:user
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> lighting fillDirection 0.2,-0.2-,-0.959
+Invalid "fillDirection" argument: Expected a number
+> lighting fillDirection 0.2,-0.2,-0.959
+> lighting fillDirection -0.2,-0.2,-0.959
+> lighting fillDirection 0.2,-0.2,-0.959
+> lighting fillDirection -0.2,-0.2,-0.959
+> lighting fillDirection -0.2,0.2,-0.959
+> lighting fillDirection -0.2,-0.2,-0.959
+> lighting fillDirection -0.2,0.1,-0.959
+> lighting fillDirection -0.3,0.1,-0.959
+> lighting fillDirection -0.2,0.1,-0.959
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+——— End of log from Mon Apr 21 17:37:05 2025 ———
+opened ChimeraX session
+> view active-site-1
+Expected an objects specifier or a view name or a keyword
+> view list
+Named views: active-site, active-site-2, active-site-3
+> view active-site-3
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> label sel offset 0,0,0
+> label sel offset 0,0,5
+[Repeated 1 time(s)]
+> label sel offset 0,5,5
+> label sel offset 5,5,5
+> label sel offset 0,5,5
+> label sel offset 0,0,5
+> label sel offset 0,2,5
+[Repeated 1 time(s)]
+> label sel offset 0,2,10
+> label sel offset 0-2,2,7
+Invalid "offset" argument: Expected 'default' or 3-tuple of numbers
+> label sel offset -2,2,7
+> select clear
+> label sel bgColor white
+> select #2/B:159@OD1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> select clear
+> color #3 #00fdffff models
+> select clear
+> select add #4.2
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 3 models selected
+> select add #2
+atoms, 13112 bonds, 27 pseudobonds, 1050 residues, 7 models selected
+> color sel #F187EE
+> color sel byhetero
+> select subtract #2
+atoms, 6556 bonds, 10 pseudobonds, 525 residues, 3 models selected
+> color sel #BF87F1
+> color sel byhetero
+> select clear
+> color #3 #00f900ff models
+> color #3 #00fdffff models
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> color sel hot pink
+> color #2 #87F18B
+> view name active-site-1
+> color #4.2 #87F1C0
+> color #2,4.2 byhetero
+> color #2 byhetero
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> color sel hot pink
+> select clear
+> color #3 #00fdffff models
+> select clear
+> color #2.2 #00fdffff models
+> select clear
+> select #2/B:201@MN
+atom, 1 residue, 1 model selected
+> label sel text Mn(III)
+> select #2/B:143@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 16 bonds, 1 residue, 1 model selected
+> label sel height 0.7
+> label sel height 0.5
+> label sel height 0.6
+> select clear
+> view name active-site-1
+> select $4.2/d
+Expected an objects specifier or a keyword
+> select #4.2/d
+Nothing selected
+> select #4.2/b
+atoms, 3284 bonds, 5 pseudobonds, 266 residues, 2 models selected
+> ui tool show "Change Chain IDs"
+> changechains sel D
+Chain IDs of 266 residues changed
+> select #4.2/D:166@CE1
+atom, 1 residue, 1 model selected
+> select add #4.2/D:162@DG2
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select clear
+[Repeated 1 time(s)]
+> select #2/B:26@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> select #2/B:74@ND1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> select #2/B:327@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/FeSOD2 Active
+> site_3.cxs"
+——— End of log from Thu Apr 24 12:40:38 2025 ———
+opened ChimeraX session
+> color #3 deep sky blue type p
+Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
+'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
+> color #3 deep sky blue target p
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD active site
+> image_5_highres.tif" width 1173 height 1080 supersample 4
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox.cxs"
+——— End of log from Thu Apr 24 19:50:15 2025 ———
+opened ChimeraX session
+> close #1
+> rename #4 name MnSOD_ox id #1
+> rename #2 name MnSOD_ox id #1.1
+> rename #3 name ox__hbonds id #1.3
+> open 7kkw name MnSOD_red
+Summary of feedback from opening 7kkw fetched from pdb
+---
+warnings | Atom D1 is not in the residue template for MET /A:0
+Atom D is not in the residue template for LYS /A:1
+Atom D is not in the residue template for HIS /A:2
+Atom D is not in the residue template for SER /A:3
+Atom D is not in the residue template for LEU /A:4
+Atom DA is not in the residue template for PRO /A:5
+Atom D is not in the residue template for ASP /A:6
+Atom D is not in the residue template for LEU /A:7
+Atom DA is not in the residue template for PRO /A:8
+Too many hydrogens missing from residue template(s) to warn about
+MnSOD_red title:
+Neutron structure of Reduced Human MnSOD [more info...]
+Chain information for MnSOD_red #2
+---
+Chain | Description | UniProt
+A B | Superoxide dismutase [Mn], mitochondrial | SODM_HUMAN 1-198
+Non-standard residues in MnSOD_red #2
+---
+D8U — deuterium(1+)
+MN — manganese (II) ion
+MnSOD_red mmCIF Assemblies
+---
+| author_and_software_defined_assembly
+> sym # 2 assembly 1
+Made 2 copies for MnSOD_red assembly 1
+> close #2
+> rename #3 name MnSOD_red id #2
+> ui tool show Matchmaker
+> matchmaker #!2.1 to #1.1 bring #!2.2
+Computing secondary structure
+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 MnSOD_ox, chain B (#1.1) with MnSOD_red, chain A (#2.1), sequence
+alignment score = 1082.2
+RMSD between 198 pruned atom pairs is 0.261 angstroms; (across all 199 pairs:
+.320)
+> select #1 & @@display
+atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected
+> select #2 & #1 :<1
+atoms, 12752 bonds, 20 pseudobonds, 890 residues, 4 models selected
+> select #1 & @@display
+atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected
+> select #2 & sel :<1
+atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected
+> show sel atoms
+> name frozen sh-r sel
+> select #1 & @@display
+atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected
+> name frozen sh-o sel
+> select sh-r
+atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected
+> select sh-r
+atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected
+> hide #!1 models
+> select add #2.1/A:302@O
+atoms, 608 bonds, 20 pseudobonds, 49 residues, 4 models selected
+> select up
+atoms, 610 bonds, 20 pseudobonds, 49 residues, 4 models selected
+> select add #2.1/A:541@D
+atoms, 610 bonds, 20 pseudobonds, 50 residues, 4 models selected
+> name frozen sh-r sel
+> select #2.1/A:324@D1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> hide sel atoms
+> select #2.1/A:25
+atoms, 18 bonds, 1 residue, 1 model selected
+> hide #2 & backbone & ~CA
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> hide #2 & backbone & ~@CA
+> select clear
+> select #2.1/A:25
+atoms, 18 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2.1/A:161
+atoms, 25 bonds, 1 residue, 1 model selected
+> select clear
+> cartoon #2 suppressBackboneDisplay false
+> hbonds #2 sh-r & ~backbond restrict #2 rev t interSubmodel t name red_hbonds
+Expected a keyword
+> hbonds sh-r & ~backbond restrict #2 rev t interSubmodel t name red_hbonds
+Expected a keyword
+> select sh-r & ~backbone
+atoms, 394 bonds, 20 pseudobonds, 50 residues, 4 models selected
+> hbonds sel restrict #2 reveal true interSubmodel true name red_hbonds
+hydrogen bonds found
+> select #2.1/A:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select #2.2/A:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select add #2.2/A:166
+atoms, 34 bonds, 2 residues, 1 model selected
+> select ~sel & ##selected
+atoms, 6489 bonds, 32 pseudobonds, 521 residues, 3 models selected
+> hide sel atoms
+> select #2.1/A:166
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #2.1/A:162
+atoms, 34 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> view active-site-1
+[Repeated 1 time(s)]
+> select #2.1/A:357@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select #2.1/A:338@O
+atom, 1 residue, 1 model selected
+> select add #2.1/A:326@O
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> select #2 & hbondatoms & @@display
+Nothing selected
+> select hbondatoms & @@display
+Nothing selected
+> select hbondatoms
+Nothing selected
+> select hbondatoms
+Nothing selected
+> select #2 & pbondatoms & @@display
+atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> select #2 & pbondatoms & @@display
+atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected
+> select clear
+> select add #3
+pseudobonds, 1 model selected
+> select up
+pseudobonds, 3 models selected
+> select up
+pseudobonds, 3 models selected
+> select up
+pseudobonds, 3 models selected
+> select up
+pseudobonds, 3 models selected
+> select down
+pseudobonds, 1 model selected
+> select down
+pseudobonds, 1 model selected
+> select clear
+> select #2 & pbondatoms & @@display
+atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected
+> select subtract #2.1/A:201@MN
+atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected
+> select subtract #2.1/A:26@NE2
+atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected
+> select subtract #2.1/A:163@NE2
+atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected
+> select subtract #2.1/A:317@O
+atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected
+> select subtract #2.1/A:74@NE2
+atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected
+> select subtract #2.1/A:30@NE2
+atoms, 1 bond, 24 pseudobonds, 28 residues, 4 models selected
+> select subtract #2.2/A:166@OH
+atoms, 1 bond, 23 pseudobonds, 27 residues, 4 models selected
+> select add #2.2/A:166@OH
+atoms, 1 bond, 23 pseudobonds, 28 residues, 4 models selected
+> hbonds sel restrict both reveal true interSubmodel true name red_hbonds
+hydrogen bonds found
+> select up
+atoms, 404 bonds, 5 pseudobonds, 28 residues, 3 models selected
+> hbonds sel restrict both interSubmodel true name red_hbonds
+hydrogen bonds found
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select clear
+> rename #3 id 2.3
+> select clear
+> ui tool show "Selection Inspector"
+> setattr sel g halfbond true
+Assigning halfbond attribute to 1 item
+> setattr sel g radius 0.155
+Assigning radius attribute to 1 item
+> style sel dashes 0
+Changed 1 pseudobond dash
+> select clear
+> select #2.1/A:317@O
+atom, 1 residue, 1 model selected
+> select add #2.1/A:501@D
+atoms, 2 residues, 1 model selected
+> pbond sel dashes 0 name shared-H
+> select subtract #2.1/A:501@D
+atom, 1 residue, 1 model selected
+> select #2.1/A:501@D
+atom, 1 residue, 1 model selected
+> select add #2.1/A:143@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel dashes 0 name shared-H
+> select #2.1/A:30@NE2
+atom, 1 residue, 1 model selected
+> select add #2.1/A:541@D
+atoms, 2 residues, 1 model selected
+> pbond sel dashes 0 name shared-H
+> select #2.1/A:541@D
+atom, 1 residue, 1 model selected
+> select add #2.2/A:166@OH
+atoms, 2 residues, 2 models selected
+> pbond sel dashes 0 name shared-H
+> combine #2.1.2#3 close true modelID 2.1.2
+Expected a keyword
+> combine #2.1.2#3 close true modelId 2.1.2
+No structures specified
+> select add #2.1.2
+atoms, 3 pseudobonds, 2 residues, 3 models selected
+> select add #3
+atoms, 4 pseudobonds, 2 residues, 4 models selected
+> select add #2.1
+atoms, 6523 bonds, 33 pseudobonds, 524 residues, 6 models selected
+> select subtract #2.1
+atom, 1 residue, 1 model selected
+> select add #2.2
+atoms, 6523 bonds, 12 pseudobonds, 523 residues, 3 models selected
+> select subtract #2.2
+Nothing selected
+> select add #2.1.2
+pseudobonds, 1 model selected
+> select add #3
+pseudobonds, 2 models selected
+> combine sel close true modelId 2.1.2
+No structures specified
+> select clear
+> rename #3 id #2.1.2
+> undo2
+Unknown command: undo2
+> undo
+> select subtract #2.1.2.1
+pseudobonds, 1 model selected
+> select add #2.1.2.1
+pseudobonds, 2 models selected
+> hide #2.1.2.1 models
+> show #2.1.2.1 models
+> ui tool show "Selection Inspector"
+> setattr sel g halfbond true
+Assigning halfbond attribute to 2 items
+> select clear
+> select #2 & pbondatoms & backbone
+atoms, 3 pseudobonds, 12 residues, 3 models selected
+> select up
+atoms, 189 bonds, 3 pseudobonds, 12 residues, 3 models selected
+> select down
+atoms, 3 pseudobonds, 12 residues, 3 models selected
+> select #2 & sel @<1
+atoms, 3 pseudobonds, 12 residues, 3 models selected
+> select #2 & sel @<1.5
+atoms, 12 bonds, 3 pseudobonds, 12 residues, 3 models selected
+> select ~sel & ::selected & ~sidechain
+atoms, 13 bonds, 12 residues, 2 models selected
+> hide sel atoms
+> hide @DA
+> ui tool show "Selection Inspector"
+> setattr =sel b display false
+Assigning display attribute to 5 items
+> select #2.1/A:70@DA3
+atom, 1 residue, 1 model selected
+> select add #2.1/A:70@DA2
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view active-site-1
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:143@O
+atom, 1 residue, 1 model selected
+> select add #2.1/A:143@C
+atoms, 1 residue, 1 model selected
+> select add #2.1/A:163@D
+atoms, 2 residues, 1 model selected
+> select add #2.1/A:163@N
+atoms, 2 residues, 1 model selected
+> hide sel atoms
+> select #2.1/A:302@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select add #2.1/A:142@O
+atoms, 2 bonds, 2 residues, 1 model selected
+> select up
+atoms, 15 bonds, 2 residues, 1 model selected
+> hide sel atoms
+> select clear
+> show #!1 models
+> hide #!1 models
+> undo
+[Repeated 4 time(s)]
+> select clear
+> select #2.1/A:29
+atoms, 21 bonds, 1 residue, 1 model selected
+> select add #2.1/A:28
+atoms, 31 bonds, 2 residues, 1 model selected
+> ui tool show "Selection Inspector"
+> setattr sel r ss_type 1
+Assigning ss_type attribute to 2 items
+> setattr sel r ss_type 0
+Assigning ss_type attribute to 2 items
+> setattr sel r ss_type 1
+Assigning ss_type attribute to 2 items
+> select clear
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+——— End of log from Fri Apr 25 13:02:38 2025 ———
+opened ChimeraX session
+> select #2.1/A:142
+atoms, 13 bonds, 1 residue, 1 model selected
+> select clear
+> select #2.1/A:501@D
+atom, 1 residue, 1 model selected
+> select add #2.1/A:317@O
+atoms, 2 residues, 1 model selected
+> select add #2.1/A:330@O
+atoms, 3 residues, 1 model selected
+> select add #2.1/A:541@D
+atoms, 4 residues, 1 model selected
+> select up
+atoms, 3 bonds, 4 residues, 1 model selected
+> style sel ball
+Changed 7 atom styles
+> select clear
+> select #2.1/A:541@D
+atom, 1 residue, 1 model selected
+> style sel stick
+Changed 1 atom style
+> style sel ball
+Changed 1 atom style
+> select clear
+> color #2.1 & C #59ECA9 target abrs
+> color #2.2 & C #59E6EC target abrs
+> select clear
+> view active-site-1
+> select #2.1/A:161@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 25 bonds, 1 residue, 1 model selected
+> ui tool show "Color Actions"
+> select intersect sidechain
+atoms, 21 bonds, 1 residue, 1 model selected
+> lighting flat
+> color sel #67ffc4ff target af
+[Repeated 3 time(s)]
+> color sel #59eca9ff target af
+> color sel #59ecaaff target af
+[Repeated 3 time(s)]
+> color sel #59eca9ff target af
+> color sel #59ecaaff target af
+[Repeated 2 time(s)]
+> color sel #59edabff target af
+[Repeated 2 time(s)]
+> color sel #59eca9ff target af
+[Repeated 1 time(s)]
+> color sel #59edaaff target af
+> color sel #5aedaaff target af
+> color sel #5aedabff target af
+[Repeated 1 time(s)]
+> color sel #8affa1ff target af
+> color sel #94c5a9ff target af
+> color sel #8cf8a3ff target af
+> color sel #95c1a8ff target af
+[Repeated 1 time(s)]
+> color sel #59eca9ff target af
+[Repeated 1 time(s)]
+> color sel #59eca9fa target af
+> color sel #59eca9f4 target af
+> color sel #59eca9e8 target af
+> color sel #59eca9d0 target af
+> color sel #59eca9ca target af
+> color sel #59eca9c7 target af
+> color sel #59eca9c2 target af
+> color sel #59eca9bd target af
+> color sel #59eca9b6 target af
+> color sel #59eca9ae target af
+> color sel #59eca9ab target af
+> color sel #59eca9a8 target af
+> color sel #59eca9a5 target af
+> color sel #59eca9a0 target af
+> color sel #59eca99e target af
+> color sel #59eca99d target af
+> color sel #59eca99b target af
+[Repeated 1 time(s)]
+> color sel #59eca99a target af
+[Repeated 1 time(s)]
+> color sel #59eca99b target af
+[Repeated 1 time(s)]
+> color sel #59eca99c target af
+[Repeated 2 time(s)]
+> color sel #59eca99d target af
+[Repeated 1 time(s)]
+> color sel #59eca99c target af
+> color sel #59eca99b target af
+> color sel #59eca998 target af
+> color sel #59eca996 target af
+> color sel #59eca98f target af
+> color sel #59eca98c target af
+> color sel #59eca985 target af
+> color sel #59eca980 target af
+> color sel byhetero target af
+> color sel #59eca97f target af
+> color sel #59eca973 target af
+> color sel #59eca968 target af
+> color sel #59eca960 target af
+> color sel #59eca958 target af
+> color sel #59eca953 target af
+> color sel #59eca950 target af
+> color sel #59eca946 target af
+> color sel #59eca943 target af
+> color sel #59eca93c target af
+> color sel #59eca939 target af
+> color sel #59eca933 target af
+> color sel #59eca92e target af
+> color sel #59eca92a target af
+> color sel #59eca929 target af
+> color sel #59eca927 target af
+> color sel #59eca926 target af
+[Repeated 1 time(s)]
+> color sel #59eca925 target af
+> color sel #59eca926 target af
+[Repeated 1 time(s)]
+> color sel #59eca927 target af
+[Repeated 2 time(s)]
+> color sel #59eca928 target af
+> color sel #59eca929 target af
+> color sel #59eca92b target af
+> color sel #59eca930 target af
+> color sel #59eca937 target af
+> color sel #59eca93b target af
+> color sel #59eca947 target af
+> color sel #59eca94f target af
+> color sel #59eca957 target af
+> color sel #59eca961 target af
+> color sel #59eca968 target af
+> color sel #59eca96f target af
+> color sel #59eca974 target af
+> color sel #59eca978 target af
+> color sel #59eca979 target af
+> color sel #59eca97a target af
+> color sel #59eca97d target af
+> color sel #59eca980 target af
+> color sel #59eca989 target af
+> color sel #59eca99e target af
+> color sel #59eca9ed target af
+> color sel #59eca9ff target af
+> color sel #59eca9ef target af
+> color sel #59eca9d9 target af
+> color sel #59eca9b0 target af
+> color sel #59eca9a1 target af
+> color sel #59eca992 target af
+> color sel #59eca97a target af
+> color sel #59eca976 target af
+> color sel #59eca972 target af
+> color sel #59eca96d target af
+> color sel #59eca96b target af
+> color sel #59eca96a target af
+[Repeated 1 time(s)]
+> color sel #59eca96b target af
+[Repeated 1 time(s)]
+> color sel #59eca96c target af
+> color sel #59eca96d target af
+> color sel #59eca96e target af
+[Repeated 1 time(s)]
+> color sel #59eca96f target af
+[Repeated 1 time(s)]
+> color sel #59eca970 target af
+> color sel #59eca971 target af
+> color sel #59eca973 target af
+> color sel #59eca976 target af
+> color sel #59eca977 target af
+> color sel #59eca97a target af
+> color sel #59eca97d target af
+> color sel #59eca980 target af
+> color sel byhetero target af
+> select clear
+> view active-site-1
+> lighting full
+> lighting shadows false
+> lighting simple
+> lighting full
+> lighting shadows false
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> view active-site-1
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select #1.1/B:143@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 16 bonds, 1 residue, 1 model selected
+> select & sidechain
+Expected an objects specifier or a keyword
+> select sel & sidechain
+atoms, 12 bonds, 1 residue, 1 model selected
+> show sel atoms
+> select clear
+> select #1.1/B:143@DA
+atom, 1 residue, 1 model selected
+> hide sel cartoons
+> view active-site-1
+> select clear
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> select #1.1/B:144
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #1.1/B:143@CB
+atom, 1 residue, 1 model selected
+> show sel cartoons
+> select #1.1/B:143@DA
+atom, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view active-site-1
+[Repeated 1 time(s)]
+> select C & @@displayed
+Nothing selected
+> select C
+atoms, 6544 bonds, 1592 residues, 4 models selected
+> select C & @@display
+atoms, 292 bonds, 60 residues, 4 models selected
+> select @D* & ((C & @@displayed) @:< 1.5)
+Expected a keyword
+> select (C & @@displayed) @:< 1.5
+Expected a keyword
+> select @D* & ((C & @@displayed) @< 1.5)
+Nothing selected
+> select (C & @@displayed) @< 1.5
+Nothing selected
+> select C & @@displayed
+Nothing selected
+> select @D* & ((C & @@display) @< 1.5)
+atoms, 84 residues, 4 models selected
+> hide sel & #!1.1-2 atoms
+> select clear
+> view active-site-1
+> select @D* & ((C & @@display) @< 1.5)
+atoms, 84 residues, 4 models selected
+> name "carbon Ds" @D* & ((C & @@display) @< 1.5)
+Not registering illegal selector name "carbon Ds"
+> name CDs @D* & ((C & @@display) @< 1.5)
+> select clear
+> view active-site-1
+> view active-site-2
+> view active-site-3
+> view active-site-1
+> view active-site-3
+> view active-site
+> view active-site-3
+> view active-site-1
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 11 bonds, 1 residue, 1 model selected
+> label sel bgColor nonw
+Invalid "bgColor" argument: Expected 'none' or a color
+> label sel bgColor none
+> select clear
+> view active-site-1
+[Repeated 1 time(s)]
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox_no-CDs.tif"
+> width 1424 height 1080 supersample 4
+> view name active-site
+> show #!2 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide CDs
+> show CDs
+> hide CDs & (@DA | :GLY)
+> select clear
+> view active-site
+> select :* & @@display & ~backbone
+atoms, 659 bonds, 51 pseudobonds, 97 residues, 11 models selected
+> select #2:* & @@display & ~backbone
+atoms, 278 bonds, 24 pseudobonds, 48 residues, 6 models selected
+> label (#!2.1-2 & sel) text "{0.name} {0.number}{0.insertion_code}"
+> label (#!2.1-2 & sel) text "{0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select #2.3:* & @@display & ~backbone
+Nothing selected
+> select #2.2:* & @@display & ~backbone
+atoms, 22 bonds, 17 residues, 1 model selected
+> ~label sel residues
+> select #2.2/A:166@CD1
+atom, 1 residue, 1 model selected
+> select add #2.2/A:162@CG
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> ui tool show "Change Chain IDs"
+> select #2.2/a
+atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected
+> select add #2.2
+atoms, 6523 bonds, 12 pseudobonds, 523 residues, 4 models selected
+> select #2.2/a
+atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected
+> ui tool show "Change Chain IDs"
+> changechains sel D
+Chain IDs of 261 residues changed
+> select #2.2/d
+atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected
+> select #2.2/D:162@CG
+atom, 1 residue, 1 model selected
+> select add #2.2/D:166@CE1
+atoms, 2 residues, 1 model selected
+> select up
+atoms, 34 bonds, 2 residues, 1 model selected
+> label sel text "/{0.chain_id} {0.label_one_letter_code}
+> {0.number}{0.insertion_code}"
+> select #2.1/A:541@D
+atom, 1 residue, 1 model selected
+> select add #2.1/A:501@D
+atoms, 2 residues, 1 model selected
+> ~label sel residues
+> select #2.1/A:330@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel text "WAT 2"
+> select #2.1/A:317@D1
+atom, 1 residue, 1 model selected
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel text "WAT 1"
+> label sel height 0.6
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> select up
+atoms, 3251 bonds, 261 residues, 1 model selected
+> select down
+atom, 1 residue, 1 model selected
+> label sel text Mn(II)
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:330@O
+atom, 1 residue, 1 model selected
+> select up
+atoms, 2 bonds, 1 residue, 1 model selected
+> label sel height 0.6
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> label sel offset 0,0,5
+> select clear
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:143@CD
+atom, 1 residue, 1 model selected
+> select up
+atoms, 15 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> show #!1 models
+> hide #!1 models
+> label sel bgColor white height 0.6
+> select up
+atoms, 1 bond, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel bgColor white
+> show #!1 models
+> hide #!1 models
+> hide #1.1.3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red.tif" width
+> 1117 height 1080 supersample 4
+> hide #!2 models
+> show #!1 models
+> show #1.1.3 models
+> hide #2.1.3 models
+> select #1.1/B:143@O
+atom, 1 residue, 1 model selected
+> select add #1.1/B:143@C
+atoms, 1 residue, 1 model selected
+> hide sel atoms
+> select clear
+> view name active-site
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox.tif" width 1117
+> height 1080 supersample 4
+> hide CDs
+> show #2.1.3 models
+> hide #2.1.3 models
+> show #2.1.3 models
+> hide #2.2.2 models
+> hide #2.1.3 models
+> hide #!2 models
+> view active-site
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Ox_no-CDs.tif"
+> width 1117 height 1080 supersample 4
+> hide #1.1.3 models
+> hide #1.2.2 models
+> hide #!1 models
+> show #!2 models
+> show #2.1.3 models
+> show #2.2.2 models
+> select #2.1/A:165
+atoms, 21 bonds, 1 residue, 1 model selected
+> select add #2.1/A:166
+atoms, 41 bonds, 2 residues, 1 model selected
+> hide sel cartoons
+> select clear
+> view name active-site_red
+> select #2.1/A:162
+atoms, 14 bonds, 1 residue, 1 model selected
+> select up
+atoms, 68 bonds, 4 residues, 1 model selected
+> show sel cartoons
+> select up
+atoms, 3153 bonds, 199 residues, 1 model selected
+> show sel cartoons
+> select clear
+> select #2.1/A:74@CG
+atom, 1 residue, 1 model selected
+> select up
+atoms, 17 bonds, 1 residue, 1 model selected
+> label sel bgColor none
+> select clear
+> view name active-site_red
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> label sel height 0.65
+> select clear
+> view name active-site_red
+> select clear
+> select #2.1/A:201@MN
+atom, 1 residue, 1 model selected
+> label sel height 0.7
+> select clear
+[Repeated 2 time(s)]
+> select #2.1/A:180
+atoms, 18 bonds, 1 residue, 1 model selected
+> hide sel atoms
+> hide sel cartoons
+> select clear
+> view name active-site_red
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_Red_no-CDs_alt-
+> view.tif" width 1117 height 1080 supersample 4
+> view name active-site-1
+> view active-site
+> view active-site_red
+> hide #!2 models
+> show #!1 models
+> show #1.1.3 models
+> show #1.2.2 models
+> show #!2 models
+> hide #!2 models
+> view active-site_red
+> hide #!1 models
+> show #!2 models
+> hide #1.1.3 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+——— End of log from Fri Apr 25 14:20:33 2025 ———
+opened ChimeraX session
+> select #2.1/b:34
+atoms, 20 bonds, 1 residue, 1 model selected
+> view sel
+> view active-site-3
+> select add #2.1/A:22
+atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected
+> select clear
+> select #2.1/A:22
+atoms, 18 bonds, 1 residue, 1 model selected
+> select clear
+[Repeated 2 time(s)]
+> select add #2.1.2
+pseudobonds, 2 models selected
+> style sel dashes 12
+Changed 2 pseudobond dashes
+> select clear
+> view active-site-3
+> select add #2.1.1
+pseudobonds, 1 model selected
+> select subtract #2.1.1
+Nothing selected
+> select add #2.1.2
+pseudobonds, 2 models selected
+> style sel dashes 10
+Changed 2 pseudobond dashes
+> select clear
+> select add #2.1.2
+pseudobonds, 2 models selected
+> style sel dashes 5
+Changed 2 pseudobond dashes
+> style sel dashes 2
+Changed 2 pseudobond dashes
+> style sel dashes 3
+Changed 2 pseudobond dashes
+> style sel dashes 4
+Changed 2 pseudobond dashes
+> style sel dashes 8
+Changed 2 pseudobond dashes
+> style sel dashes 12
+Changed 2 pseudobond dashes
+> style sel dashes 35
+Changed 2 pseudobond dashes
+> style sel dashes 20
+Changed 2 pseudobond dashes
+> style sel dashes 10
+Changed 2 pseudobond dashes
+> select clear
+> hide #2.1.3 models
+> show #2.1.3 models
+> hide #2.3 models
+> hide #2.1.3 models
+> show #2.1.3 models
+> show #2.3 models
+> hide #2.2.2 models
+> show CDs
+> show list
+Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
+'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
+> name list
+CDs @D* & ((C & @@display) @< 1.5)
+both_shell (ox_shell | red_shell)
+sh-o [482 atoms, 466 bonds, 5 models]
+sh-r [627 atoms, 610 bonds, 4 models]
+> hide @DA*
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active site.cxs"
+> combine #2 retainIds true
+'retainIds' requires residues number / insertion code combos be unique in each
+chain with the same ID (duplicate: /B MET 0)
+> combine #2 retainIds true modelId #3
+'retainIds' requires residues number / insertion code combos be unique in each
+chain with the same ID (duplicate: /B MET 0)
+> combine #2 modelId #3
+Remapping chain ID 'B' in MnSOD_red #2.2 to 'C'
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> select add #2
+atoms, 13046 bonds, 48 pseudobonds, 1046 residues, 10 models selected
+> select subtract #2
+Nothing selected
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> hide #3.2 models
+> show #3.2 models
+> hide #3.2 models
+> show #3.2 models
+> hide #3.1 models
+> show #3.1 models
+> hide #!2.1 models
+> show #!2.1 models
+> hide #!2 models
+> hide #!3 models
+> show #!3 models
+> select add #3
+atoms, 13046 bonds, 25 pseudobonds, 1046 residues, 3 models selected
+> ui tool show "Change Chain IDs"
+> changechains sel D C
+Proposed chainID change conflicts with existing residue combination #3/C MET 0
+> changechains sel C,D D,C
+Chain IDs of 523 residues changed
+> select add #2.1
+atoms, 19569 bonds, 58 pseudobonds, 1569 residues, 9 models selected
+> select subtract #2.1
+atoms, 13046 bonds, 25 pseudobonds, 1046 residues, 3 models selected
+> show #!2 models
+> changechains #2.1 A,B B,A
+Chain IDs of 523 residues changed
+> select subtract #3
+Nothing selected
+> select add #3.1
+pseudobonds, 1 model selected
+> select subtract #3.1
+Nothing selected
+> hide #!3 models
+> show #!3 models
+> mcopy #2.1 toAtoms #3 settings csvlp
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #3.3 models
+> show #3.3 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> view active-site-3
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!3 models
+> show #!3 models
+> hide #!3 models
+> show #!3 models
+> hide #!2 models
+> show #!2 models
+> mcopy #2.1 toAtoms #3 settings csvly
+> mcopy #2.1 toAtoms #3 settings csvlxy
+> mcopy #2.1 toAtoms #3 settings csvlxpy
+> mcopy #2.1 toAtoms #3 settings csvlxp
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> show #!2 models
+> hide #!2 models
+> close #3
+> show #!2 models
+> hide #2.3 models
+> show #2.3 models
+> changechains #2.1 A,B B,A
+Chain IDs of 523 residues changed
+> select add #2.2
+atoms, 6523 bonds, 12 pseudobonds, 523 residues, 4 models selected
+> ui tool show "Change Chain IDs"
+> select clear
+> hide #2.3 models
+> show #2.3 models
+> changechains #2.2 B,D D,C
+Chain IDs of 523 residues changed
+> select clear
+> combine #2 modelId #3
+> hide #3.1 models
+> show #3.1 models
+> hide #!2 models
+> hide #!3 models
+> show #!3 models
+> show #!1 models
+> hide #!1 models
+> show #!2 models
+> hide #!2 models
+> ui tool show Matchmaker
+> matchmaker #3/B to #2.1/A pairing ss
+Parameters
+---
+Chain pairing | ss
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker MnSOD_red, chain A (#2.1) with combination, chain B (#3), sequence
+alignment score = 1082.8
+RMSD between 198 pruned atom pairs is 0.240 angstroms; (across all 199 pairs:
+.292)
+> show #!2 models
+> hide #!2 models
+> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
+> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD Active
+> site_WIP.cxs"
+——— End of log from Fri Apr 25 16:51:41 2025 ———
+opened ChimeraX session
+> select #3/B:201@MN
+atom, 1 residue, 1 model selected
+> cofr sel
+> select #3/B:34@OH
+atom, 1 residue, 1 model selected
+> select add #3/B:566@D
+atoms, 2 residues, 1 model selected
+> bond sel
+Created 1 bond
+> select clear
+> mcopy #2.1/a & protein toAtoms #3/b target csvl match f
+Expected a keyword
+> mcopy #2.1/a & protein toAtoms #3/b settings csvl matchResidues false
+> show #!2 models
+> hide #!2 models
+> mcopy #2.2/c toAtoms #3/d settings csvl matchResidues false
+> select add #3/D:166
+atoms, 20 bonds, 1 residue, 1 model selected
+> select add #3/D:162
+atoms, 34 bonds, 2 residues, 1 model selected
+> select up
+atoms, 191 bonds, 10 residues, 1 model selected
+> select up
+atoms, 3160 bonds, 199 residues, 1 model selected
+> select subtract #3/D:162
+atoms, 3144 bonds, 198 residues, 1 model selected
+> select subtract #3/D:166
+atoms, 3122 bonds, 197 residues, 1 model selected
+> hide sel atoms
+> select clear
+> ui mousemode right "move label"
+> hide #3/a,c
+> select clear
+> select #3/B:181
+atoms, 25 bonds, 1 residue, 1 model selected
+> select up
+atoms, 184 bonds, 10 residues, 1 model selected
+> show sel cartoons
+> select clear
+> hbonds #3 & @@display restrict both interModel false name red_hbonds
+hydrogen bonds found
+> delete sel
+> ~bond sel
+> delete pbonds sel
+[Repeated 1 time(s)]
+> select clear
+> select add #3/B:143@NE2
+atom, 1 bond, 1 residue, 1 model selected
+> pbond sel color deep sky blue name red_hbonds
+Must specify exactly 2 atoms to form pseudobond between; you specified 1
+> select #3/B:319@D2
+atom, 1 residue, 1 model selected
+> select add #3/B:143@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel color deep sky blue name red_hbonds
+Pseudobond group 'red_hbonds' already exists as a per-coordset group
+> pbond sel color deep sky blue
+> select clear
+> close #3.2
+> select #3/D:166@OH
+atom, 1 residue, 1 model selected
+> select add #3/B:540@D
+atoms, 2 residues, 1 model selected
+> pbond sel name shared-H
+> select #3/B:30@NE2
+atom, 1 residue, 1 model selected
+> select #3/B:540@D
+atom, 1 residue, 1 model selected
+> select add #3/B:30@NE2
+atoms, 2 residues, 1 model selected
+> pbond sel name shared-H
+> select add #3.2
+atoms, 2 pseudobonds, 2 residues, 2 models selected
+[deleted to fit within ticket limits]
 > ui tool show "Selection Inspector"