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Opened 8 weeks ago

Last modified 8 weeks ago

#18644 closed defect

ChimeraX bug report submission — at Initial Version

Reported by:	chimerax-bug-report@…	Owned by:
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Tried to open another session file with combine = true

Log:
UCSF 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 Wed Aug 27 15:48:40 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/Figs_V3/MnSOD.cxs"
> format session

Not registering illegal selector name "carbon Ds"  

Log from Wed Aug 27 15:43:32 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  
  
434 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add sel @< 10

409 atoms, 372 bonds, 57 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select sel @< 5

47 atoms, 37 bonds, 12 residues, 1 model selected  

> show sel atoms

> select up

178 atoms, 176 bonds, 12 residues, 1 model selected  

> show sel atoms

> select /A:71

17 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

1 atom, 1 residue, 1 model selected  

> select /A:163@NE2

1 atom, 1 residue, 1 model selected  

> select add /D:4@FE

2 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

372 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*

2674 atoms, 396 residues, 1 model selected  

> hide sel atoms

> select clear

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> view sel

> ui tool show H-Bonds

> hbonds reveal true

2448 hydrogen bonds found  

> undo

> redo

> ~hbonds

> hbonds sel reveal true

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel reveal true

0 hydrogen bonds found  

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select sel @< 5

47 atoms, 37 bonds, 12 residues, 1 model selected  

> select up

168 atoms, 166 bonds, 12 residues, 1 model selected  

> select ~sel

6368 atoms, 5742 bonds, 1086 residues, 1 model selected  

> hide sel atoms

> select ~sel & ##selected

168 atoms, 184 bonds, 12 residues, 1 model selected  

> select @H*

2674 atoms, 396 residues, 1 model selected  

> hide sel atoms

> select clear

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true

2 hydrogen bonds found  

> select @H*

2674 atoms, 396 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true

2 hydrogen bonds found  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select /A:163@NE2

1 atom, 1 residue, 1 model selected  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:163@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:26@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:74@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:159@OD2

2 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

1 atom, 1 residue, 1 model selected  

> select /A:123@NE1

1 atom, 1 residue, 1 model selected  

> select add /A:143@CD

2 atoms, 2 residues, 1 model selected  

> select up

23 atoms, 23 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 restrict both reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select /A:34@CZ

1 atom, 1 residue, 1 model selected  

> select /A:34@OH

1 atom, 1 residue, 1 model selected  

> select add /A:30@ND1

2 atoms, 2 residues, 1 model selected  

> select add /A:30@NE2

3 atoms, 2 residues, 1 model selected  

> select add /A:163@ND1

4 atoms, 3 residues, 1 model selected  

> select add /A:26@ND1

5 atoms, 4 residues, 1 model selected  

> select add /A:74@ND1

6 atoms, 5 residues, 1 model selected  

> select add /A:159@OD1

7 atoms, 6 residues, 1 model selected  

> select add /A:161@NE1

8 atoms, 7 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

11 hydrogen bonds found  

> select clear

> select /S:229@O

1 atom, 1 residue, 1 model selected  

> select add /S:12@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> hide sel

> select clear

> hide sel

> select clear

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /E:2@O

2 atoms, 2 residues, 1 model selected  

> hbonds sel

2 hydrogen bonds found  

> undo

> select /A:143@NE2

1 atom, 1 residue, 1 model selected  

> select add /S:263@O

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

9 hydrogen bonds found  

> select /S:229@O

1 atom, 1 residue, 1 model selected  

> select add /S:110@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select /A:143@OE1

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

2 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

1 atom, 1 residue, 1 model selected  

> select add /E:2@O

2 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

9 atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract /A:187

2 pseudobonds, 1 model selected  

> select add /A:187

9 atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract /A:187

3 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

1 atom, 1 residue, 1 model selected  

> view sel

> cofr sel

> select clear

> select /A:161@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select clear

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> select add /S:263@O

2 atoms, 2 residues, 1 model selected  

> style sel ball

Changed 2 atom styles  

> select clear

> help help:user

> surface cap true

> select /A:120

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

> select add /A:121

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

> select add /A:122

14 atoms, 11 bonds, 3 residues, 1 model selected  

> select add /A:123

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select subtract /A:123

14 atoms, 11 bonds, 3 residues, 1 model selected  

> select add /A:141

21 atoms, 18 bonds, 4 residues, 1 model selected  

> select subtract /A:141

14 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

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

> select /A:163

10 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

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.4.1

1 model selected  

> select subtract #1.4.1

Nothing selected  

> select add #1.4.2

1 model selected  

> select subtract #1.4.2

Nothing selected  

> select add #1.3.1

1 model selected  

> select add #1.3.2

2 models selected  

> select subtract #1.3.2

1 model selected  

> select add #1.3.2

2 models selected  

> select subtract #1.3.1

1 model selected  

> select subtract #1.3.2

Nothing selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> hide #1.3.1 models

> show #1.3.1 models

> select subtract #1.3.1

1574 atoms, 198 residues, 3 models selected  

> select add #1.3.1

1574 atoms, 198 residues, 4 models selected  

> select subtract #1.3

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> hide #!1.4 target m

> hide #!1.3 models

> show #1.3 models

> select add #1.3

1574 atoms, 198 residues, 1 model selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 1 model selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 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  
  
7kks 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  
  
7kks mmCIF Assemblies  
---  
1| 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:
0.393)  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select clear

> select #2/B:161@CG

1 atom, 1 residue, 1 model selected  

> select up

24 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

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@NE2

2 atoms, 2 residues, 1 model selected  

> select up

19 atoms, 17 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

12 hydrogen bonds found  

> select #2/B:73@ND2

1 atom, 1 residue, 1 model selected  

> select up

14 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #2/B:30

36 atoms, 36 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #2/B:34@OH

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

5 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

3863 atoms, 3252 bonds, 17 pseudobonds, 1099 residues, 4 models selected  

> select subtract #1

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

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@DE22

2 atoms, 2 residues, 1 model selected  

> select clear

> show #!1 models

> hide #!1 models

> select add #2/B:74@NE2

1 atom, 4 pseudobonds, 1 residue, 2 models selected  

> select clear

> select #2/B:201@MN

1 atom, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> select up

3305 atoms, 3284 bonds, 266 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select add #2/B:74@NE2

1 atom, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract #2/B:74@NE2

2 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

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

> hide sel cartoons

> select clear

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #2/B:160

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select add #2/B:162

55 atoms, 54 bonds, 3 residues, 1 model selected  

> select add #2/B:163

72 atoms, 71 bonds, 4 residues, 1 model selected  

> select clear

> select #2/B:162

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

> select add #2/B:161

39 atoms, 39 bonds, 2 residues, 1 model selected  

> select subtract #2/B:161

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

> select add #2/B:161

39 atoms, 39 bonds, 2 residues, 1 model selected  

> select add #2/B:160

55 atoms, 54 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #2/B:121

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

> hide sel

> hide sel cartoons

> select clear

> select #2/B:162

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

> show sel cartoons

> select #2/B:161-150

Nothing selected  

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select #2/B:160

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

> show sel atoms

> select #2/B:160

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

> hide sel atoms

> show sel cartoons

> select clear

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #2/B:160

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select add #2/B:141

54 atoms, 54 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #2/B:327@O

1 atom, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 2 atom styles  

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select up

3 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:
0.000)  
  

> 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4.2/B:162

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

> show sel atoms

> select #4.2/B:166@CZ

1 atom, 1 residue, 1 model selected  

> select add #4.2/B:162@CD

2 atoms, 2 residues, 1 model selected  

> select add #2/B:163@ND1

3 atoms, 1 bond, 3 residues, 2 models selected  

> select up

5 atoms, 1 bond, 4 residues, 2 models selected  

> select up

68 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

4 hydrogen bonds found  

> select #4.2/B:120

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

> select #4.2/B:119

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #4.2/B:120

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

> select add #4.2/B:121

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select add #4.2/B:119

35 atoms, 32 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #2/B:201@MN

1 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

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/B:201@MN

1 atom, 1 residue, 1 model selected  

> hide sel

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

3 hydrogen bonds found  

> select clear

> select #2/B:34@CZ

1 atom, 1 residue, 1 model selected  

> select #2/B:143@DE22

1 atom, 1 residue, 1 model selected  

> select #2/B:34@OH

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@DE22

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 restrict both reveal true retainCurrent
> true

0 hydrogen bonds found  

> select clear

> select #2/B:201@MN

1 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/B:123@CD1

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/B:74@CE1

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

34 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

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select add #2/B:327@O

2 atoms, 2 residues, 1 model selected  

> select up

5 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

6591 atoms, 6556 bonds, 10 pseudobonds, 525 residues, 2 models selected  

> color (#!4.2 & sel) byhetero

> select subtract #4.2

Nothing selected  

> select add #3

23 pseudobonds, 1 model selected  

> color #3 #ff40ffff models

> select clear

> select #2/B:201@MN

1 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

1 model selected  

> ui tool show "Selection Inspector"

> select subtract #2.3

Nothing selected  

> select add #2.3

1 model selected  
No visible atoms selected  

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 2"

> select #2/B:327@O

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text "WAT 1"

> label sel text WAT1

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text WAT2

> select #2/B:201@MN

1 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

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #2/B:68

20 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

6591 atoms, 6556 bonds, 16 pseudobonds, 525 residues, 4 models selected  

> select add #4

13182 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

1 atom, 2 bonds, 1 residue, 2 models selected  

> select add #2/B:163@DB2

2 atoms, 2 bonds, 2 residues, 2 models selected  

> select add #2/B:163@CE1

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

> select add #2/B:336@O

4 atoms, 5 bonds, 3 residues, 2 models selected  

> select add #2/B:327@O

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

> select add #2/B:123@CZ2

6 atoms, 6 bonds, 5 residues, 2 models selected  

> select add #2/B:143@CG

7 atoms, 6 bonds, 6 residues, 2 models selected  

> select add #2/B:73@CB

8 atoms, 6 bonds, 7 residues, 2 models selected  

> select up

20 atoms, 6 bonds, 13 residues, 2 models selected  

> select up

201 atoms, 197 bonds, 13 residues, 2 models selected  

> select up

203 atoms, 198 bonds, 14 residues, 2 models selected  

> select up

218 atoms, 215 bonds, 14 residues, 2 models selected  

> select add #2/B:201@MN

219 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

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

> select up

35 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 2"

> select up

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

> label sel text "WAT 2"

> label sel text "WAT 1"

> select #2/B:201@MN

1 atom, 1 residue, 1 model selected  

> label sel text Mn

> select clear

> select #2/B:142

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select add #2/B:143

31 atoms, 29 bonds, 2 residues, 1 model selected  

> select add #2/B:144

43 atoms, 40 bonds, 3 residues, 1 model selected  

> help help:user

> select clear

> select #2/B:143

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2/B:142

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/B:144

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #2/B:142

26 atoms, 24 bonds, 2 residues, 1 model selected  

> select add #2/B:143

43 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

1 atom, 1 residue, 1 model selected  

> select up

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

> select #2/B:327@D2

1 atom, 1 residue, 1 model selected  

> select #2/B:159@OD1

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

2 hydrogen bonds found  

> select clear

> select #2/B:161

24 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

1 atom, 1 residue, 1 model selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@N

2 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

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@C

2 atoms, 1 residue, 1 model selected  

> select add #2/B:161@CA

3 atoms, 1 residue, 1 model selected  

> select add #2/B:161@DA

4 atoms, 1 residue, 1 model selected  

> select subtract #2/B:161@CA

3 atoms, 1 residue, 1 model selected  

> select add #2/B:161@CA

4 atoms, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/B:143

17 atoms, 16 bonds, 1 residue, 1 model selected  

> ribbon sel suppressBackboneDisplay false

> select #2/B:143@D

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@N

2 atoms, 1 residue, 1 model selected  

> select subtract #2/B:143

Nothing selected  

> select #2/B:143

17 atoms, 16 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #2/B:143@C

1 atom, 1 residue, 1 model selected  

> select #2/B:143@CA

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@D

2 atoms, 1 residue, 1 model selected  

> select add #2/B:143@N

3 atoms, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> show sel atoms

> select #2/B:143@D

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@N

2 atoms, 1 residue, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select #2/B:143@C

1 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

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> select #2/B:161@DA

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@C

2 atoms, 1 residue, 1 model selected  

> select add #2/B:161@O

3 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

1 atom, 1 residue, 1 model selected  

> select up

24 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select subtract #2/B:161

Nothing selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select add #2/B:161@D

1 atom, 1 pseudobond, 1 residue, 2 models selected  

> select clear

> select #2/B:161@D

1 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

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

> select #2/B:162

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

> select #2/B:161@CA

1 atom, 1 residue, 1 model selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> select #2/B:161@N

1 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

24 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

1 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

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select add #2/B:142

31 atoms, 29 bonds, 2 residues, 1 model selected  

> select subtract #2/B:143

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/B:143

17 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

31 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> select #2/B:161@CB

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select #2/B:161@O

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@C

2 atoms, 1 residue, 1 model selected  

> select add #2/B:161@DA

3 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select #2/B:180

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2/B:161@N

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2/B:161@N

1 atom, 1 residue, 1 model selected  

> select #2/B:161@CB

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select subtract #2/B:161@D

23 atoms, 24 bonds, 1 residue, 1 model selected  

> select subtract #2/B:161@N

22 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

1 atom, 1 residue, 1 model selected  

> select add #2/B:336@O

2 atoms, 2 residues, 1 model selected  

> select add #2/B:327@O

3 atoms, 3 residues, 1 model selected  

> select up

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

> select ~sel & ##selected

6585 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

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

> select up

17 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label sel bgColor white

> select up

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

> select up

12 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

1 atom, 1 residue, 1 model selected  

> select up

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

> select down

1 atom, 1 residue, 1 model selected  

> select up

2 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

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel height 0.65

> select clear

> select #2/B:144

12 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

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

> select up

12 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

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel bgColor white

> select clear

> color #3 #00fdffff models

> select clear

> select add #4.2

6591 atoms, 6556 bonds, 10 pseudobonds, 525 residues, 3 models selected  

> select add #2

13182 atoms, 13112 bonds, 27 pseudobonds, 1050 residues, 7 models selected  

> color sel #F187EE

> color sel byhetero

> select subtract #2

6591 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

1 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

1 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

1 atom, 1 residue, 1 model selected  

> label sel text Mn(III)

> select #2/B:143@CD

1 atom, 1 residue, 1 model selected  

> select up

17 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

3305 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

1 atom, 1 residue, 1 model selected  

> select add #4.2/D:162@DG2

2 atoms, 2 residues, 1 model selected  

> select up

35 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> label sel offset 0,0,5

> select #2/B:74@ND1

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> label sel offset 0,0,5

> select #2/B:327@O

1 atom, 1 residue, 1 model selected  

> select up

2 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  
---  
1| 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:
0.320)  
  

> select #1 & @@display

482 atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected  

> select #2 & #1 :<1

12662 atoms, 12752 bonds, 20 pseudobonds, 890 residues, 4 models selected  

> select #1 & @@display

482 atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected  

> select #2 & sel :<1

623 atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected  

> show sel atoms

> name frozen sh-r sel

> select #1 & @@display

482 atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected  

> name frozen sh-o sel

> select sh-r

623 atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected  

> select sh-r

623 atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected  

> hide #!1 models

> select add #2.1/A:302@O

624 atoms, 608 bonds, 20 pseudobonds, 49 residues, 4 models selected  

> select up

626 atoms, 610 bonds, 20 pseudobonds, 49 residues, 4 models selected  

> select add #2.1/A:541@D

627 atoms, 610 bonds, 20 pseudobonds, 50 residues, 4 models selected  

> name frozen sh-r sel

> select #2.1/A:324@D1

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select #2.1/A:25

19 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

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2.1/A:161

24 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

417 atoms, 394 bonds, 20 pseudobonds, 50 residues, 4 models selected  

> hbonds sel restrict #2 reveal true interSubmodel true name red_hbonds

52 hydrogen bonds found  

> select #2.1/A:162

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

> select #2.2/A:162

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

> select add #2.2/A:166

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select ~sel & ##selected

6521 atoms, 6489 bonds, 32 pseudobonds, 521 residues, 3 models selected  

> hide sel atoms

> select #2.1/A:166

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #2.1/A:162

35 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2.1/A:338@O

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:326@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select up

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

> select up

3 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

49 atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected  

> select #2.1/A:201@MN

1 atom, 1 residue, 1 model selected  

> select #2 & pbondatoms & @@display

49 atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected  

> select clear

> select add #3

52 pseudobonds, 1 model selected  

> select up

52 pseudobonds, 3 models selected  

> select up

52 pseudobonds, 3 models selected  

> select up

52 pseudobonds, 3 models selected  

> select up

52 pseudobonds, 3 models selected  

> select down

52 pseudobonds, 1 model selected  

> select down

52 pseudobonds, 1 model selected  

> select clear

> select #2 & pbondatoms & @@display

49 atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected  

> select subtract #2.1/A:201@MN

48 atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected  

> select subtract #2.1/A:26@NE2

47 atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected  

> select subtract #2.1/A:163@NE2

46 atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected  

> select subtract #2.1/A:317@O

45 atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected  

> select subtract #2.1/A:74@NE2

44 atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected  

> select subtract #2.1/A:30@NE2

43 atoms, 1 bond, 24 pseudobonds, 28 residues, 4 models selected  

> select subtract #2.2/A:166@OH

42 atoms, 1 bond, 23 pseudobonds, 27 residues, 4 models selected  

> select add #2.2/A:166@OH

43 atoms, 1 bond, 23 pseudobonds, 28 residues, 4 models selected  

> hbonds sel restrict both reveal true interSubmodel true name red_hbonds

5 hydrogen bonds found  

> select up

410 atoms, 404 bonds, 5 pseudobonds, 28 residues, 3 models selected  

> hbonds sel restrict both interSubmodel true name red_hbonds

22 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:501@D

2 atoms, 2 residues, 1 model selected  

> pbond sel dashes 0 name shared-H

> select subtract #2.1/A:501@D

1 atom, 1 residue, 1 model selected  

> select #2.1/A:501@D

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:143@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel dashes 0 name shared-H

> select #2.1/A:30@NE2

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:541@D

2 atoms, 2 residues, 1 model selected  

> pbond sel dashes 0 name shared-H

> select #2.1/A:541@D

1 atom, 1 residue, 1 model selected  

> select add #2.2/A:166@OH

2 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

2 atoms, 3 pseudobonds, 2 residues, 3 models selected  

> select add #3

2 atoms, 4 pseudobonds, 2 residues, 4 models selected  

> select add #2.1

6557 atoms, 6523 bonds, 33 pseudobonds, 524 residues, 6 models selected  

> select subtract #2.1

1 atom, 1 residue, 1 model selected  

> select add #2.2

6556 atoms, 6523 bonds, 12 pseudobonds, 523 residues, 3 models selected  

> select subtract #2.2

Nothing selected  

> select add #2.1.2

3 pseudobonds, 1 model selected  

> select add #3

4 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

3 pseudobonds, 1 model selected  

> select add #2.1.2.1

4 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

12 atoms, 3 pseudobonds, 12 residues, 3 models selected  

> select up

192 atoms, 189 bonds, 3 pseudobonds, 12 residues, 3 models selected  

> select down

12 atoms, 3 pseudobonds, 12 residues, 3 models selected  

> select #2 & sel @<1

12 atoms, 3 pseudobonds, 12 residues, 3 models selected  

> select #2 & sel @<1.5

24 atoms, 12 bonds, 3 pseudobonds, 12 residues, 3 models selected  

> select ~sel & ::selected & ~sidechain

24 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:70@DA2

2 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:143@C

2 atoms, 1 residue, 1 model selected  

> select add #2.1/A:163@D

3 atoms, 2 residues, 1 model selected  

> select add #2.1/A:163@N

4 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select #2.1/A:302@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

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

> select up

17 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

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2.1/A:28

33 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

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select clear

> select #2.1/A:501@D

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:317@O

2 atoms, 2 residues, 1 model selected  

> select add #2.1/A:330@O

3 atoms, 3 residues, 1 model selected  

> select add #2.1/A:541@D

4 atoms, 4 residues, 1 model selected  

> select up

7 atoms, 3 bonds, 4 residues, 1 model selected  

> style sel ball

Changed 7 atom styles  

> select clear

> select #2.1/A:541@D

1 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> select intersect sidechain

20 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select & sidechain

Expected an objects specifier or a keyword  

> select sel & sidechain

13 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1.1/B:143@DA

1 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

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1.1/B:143@CB

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select #1.1/B:143@DA

1 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

8104 atoms, 6544 bonds, 1592 residues, 4 models selected  

> select C & @@display

358 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)

425 atoms, 84 residues, 4 models selected  

> hide sel & #!1.1-2 atoms

> select clear

> view active-site-1

> select @D* & ((C & @@display) @< 1.5)

425 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

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

> select up

12 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

778 atoms, 659 bonds, 51 pseudobonds, 97 residues, 11 models selected  

> select #2:* & @@display & ~backbone

352 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

84 atoms, 22 bonds, 17 residues, 1 model selected  

> ~label sel residues

> select #2.2/A:166@CD1

1 atom, 1 residue, 1 model selected  

> select add #2.2/A:162@CG

2 atoms, 2 residues, 1 model selected  

> select up

35 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

3267 atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected  

> select add #2.2

6556 atoms, 6523 bonds, 12 pseudobonds, 523 residues, 4 models selected  

> select #2.2/a

3267 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

3267 atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected  

> select #2.2/D:162@CG

1 atom, 1 residue, 1 model selected  

> select add #2.2/D:166@CE1

2 atoms, 2 residues, 1 model selected  

> select up

35 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:501@D

2 atoms, 2 residues, 1 model selected  

> ~label sel residues

> select #2.1/A:330@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 2"

> select #2.1/A:317@D1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text "WAT 1"

> label sel height 0.6

> select #2.1/A:201@MN

1 atom, 1 residue, 1 model selected  

> select up

3267 atoms, 3251 bonds, 261 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> label sel text Mn(II)

> show #!1 models

> hide #!1 models

> select #2.1/A:330@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

2 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

1 atom, 1 residue, 1 model selected  

> select up

16 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

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

> select up

17 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

1 atom, 1 residue, 1 model selected  

> select add #1.1/B:143@C

2 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

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2.1/A:166

41 atoms, 41 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select clear

> view name active-site_red

> select #2.1/A:162

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

> select up

66 atoms, 68 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select up

3107 atoms, 3153 bonds, 199 residues, 1 model selected  

> show sel cartoons

> select clear

> select #2.1/A:74@CG

1 atom, 1 residue, 1 model selected  

> select up

17 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

1 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

1 atom, 1 residue, 1 model selected  

> label sel height 0.7

> select clear

[Repeated 2 time(s)]

> select #2.1/A:180

19 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> view sel

> view active-site-3

> select add #2.1/A:22

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select clear

> select #2.1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select add #2.1.2

4 pseudobonds, 2 models selected  

> style sel dashes 12

Changed 2 pseudobond dashes  

> select clear

> view active-site-3

> select add #2.1.1

11 pseudobonds, 1 model selected  

> select subtract #2.1.1

Nothing selected  

> select add #2.1.2

4 pseudobonds, 2 models selected  

> style sel dashes 10

Changed 2 pseudobond dashes  

> select clear

> select add #2.1.2

4 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

13112 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

13112 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

19668 atoms, 19569 bonds, 58 pseudobonds, 1569 residues, 9 models selected  

> select subtract #2.1

13112 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

22 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

6556 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:
0.292)  
  

> 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

1 atom, 1 residue, 1 model selected  

> cofr sel

> select #3/B:34@OH

1 atom, 1 residue, 1 model selected  

> select add #3/B:566@D

2 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #3/D:162

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select up

186 atoms, 191 bonds, 10 residues, 1 model selected  

> select up

3114 atoms, 3160 bonds, 199 residues, 1 model selected  

> select subtract #3/D:162

3099 atoms, 3144 bonds, 198 residues, 1 model selected  

> select subtract #3/D:166

3079 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

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

181 atoms, 184 bonds, 10 residues, 1 model selected  

> show sel cartoons

> select clear

> hbonds #3 & @@display restrict both interModel false name red_hbonds

11 hydrogen bonds found  

> delete sel

> ~bond sel

> delete pbonds sel

[Repeated 1 time(s)]

> select clear

> select add #3/B:143@NE2

1 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:143@NE2

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:540@D

2 atoms, 2 residues, 1 model selected  

> pbond sel name shared-H

> select #3/B:30@NE2

1 atom, 1 residue, 1 model selected  

> select #3/B:540@D

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel name shared-H

> select add #3.2

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

2 atoms, 24 pseudobonds, 2 residues, 3 models selected  

> select subtract #3.1

2 atoms, 2 pseudobonds, 2 residues, 2 models selected  

> select add #3.1

2 atoms, 24 pseudobonds, 2 residues, 3 models selected  

> select subtract #3.2

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

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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 1"

> select #3/B:348@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 3 atom styles  

> select #3/B:201@MN

1 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

13112 atoms, 13046 bonds, 48 pseudobonds, 1046 residues, 10 models selected  

> select subtract #2

Nothing selected  

> select add #2

13112 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

3289 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

6556 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

6556 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:201@MN

2 atoms, 2 residues, 1 model selected  

> ~bond sel

> delete bonds sel

> select #3/B:201@MN

1 atom, 1 residue, 1 model selected  

> select add #3/B:319@O

2 atoms, 2 residues, 1 model selected  

> delete bonds sel

> select clear

> select #3/B:143@DG3

1 atom, 1 residue, 1 model selected  

> select add #3/B:143@DB3

2 atoms, 1 residue, 1 model selected  

> bond sel

Created 0 bonds  

> select #3/B:143@DE22

1 atom, 1 residue, 1 model selected  

> select add #3/B:34@OH

2 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

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

> select clear

> select #3/B:74@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/B:74@CE1

2 atoms, 1 residue, 1 model selected  

> select #3/B:30@DB3

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@CB

2 atoms, 1 residue, 1 model selected  

> select #3/B:348@O

1 atom, 1 residue, 1 model selected  

> select add #3/B:348@D2

2 atoms, 1 residue, 1 model selected  

> ~bond sel

> bond sel

Created 1 bond  

> select #3/B:30@DD1

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@DB3

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:201@MN

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:201@MN

2 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/B:73@CB

1 atom, 1 residue, 1 model selected  

> select up

14 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

2 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1.1/B:73@CB

1 atom, 1 residue, 1 model selected  

> select #1.1/B:73@CB

1 atom, 1 residue, 1 model selected  

> select up

14 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

1 atom, 1 residue, 1 model selected  

> select sel @< 5

157 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

392 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

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select up

120 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  
  
7kks 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  
  
7kks mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select #4:166

40 atoms, 40 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #4:166

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select sel @< 5 & ~sel

1264 atoms, 1113 bonds, 166 residues, 6 models selected  

> show sel & #!4 atoms

> select up

2552 atoms, 2534 bonds, 166 residues, 6 models selected  

> show sel & #!4 atoms

> hide sel & #!4 atoms

> select clear

> select #4/B:327@O

1 atom, 1 residue, 1 model selected  

> hide #!4 models

> view y166-h30

> show #!3 models

> select #3/B:540@D

1 atom, 1 residue, 1 model selected  

> select up

3289 atoms, 3273 bonds, 262 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select clear

> select #4:his

339 atoms, 343 bonds, 20 residues, 1 model selected  

> select #3:his

680 atoms, 688 bonds, 40 residues, 1 model selected  

> select #3:D

Nothing selected  

> select #3:D8U

8 atoms, 8 residues, 1 model selected  

> select #1:D8U

Nothing selected  

> select #2:D8U

8 atoms, 8 residues, 2 models selected  

> select #4:D8U

Nothing selected  

> select #4@D8U

Nothing selected  

> select #4@D

373 atoms, 373 residues, 1 model selected  

> select #2@D

752 atoms, 752 residues, 2 models selected  

> select #2.1@D

376 atoms, 376 residues, 1 model selected  

> select #3@D

752 atoms, 752 residues, 1 model selected  

> select #3@D

752 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

373 atoms, 373 residues, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> ui tool show "Selection Inspector"

> select up

5865 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

373 atoms, 373 residues, 1 model selected  

> select #4@D*

3302 atoms, 518 residues, 1 model selected  

> show sel atoms

> select up

6584 atoms, 6556 bonds, 518 residues, 1 model selected  

> show sel atoms

> show #4 atoms

> select clear

> select #4/A:306@O

1 atom, 1 residue, 1 model selected  

> select up

3286 atoms, 3272 bonds, 259 residues, 1 model selected  

> select down

1 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

1 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

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show sel atoms

> view y166-h30

> select #1.1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1.1/A:30@DD1

1 atom, 1 residue, 1 model selected  

> select sel @< 5

178 atoms, 133 bonds, 1 pseudobond, 44 residues, 7 models selected  

> select sel & solvent

33 atoms, 20 bonds, 13 residues, 6 models selected  

> show sel & #!1.1-2 atoms

> select #1.1/A:306@O

1 atom, 1 residue, 1 model selected  

> select up

3286 atoms, 3272 bonds, 259 residues, 1 model selected  

> select #1.1/A:306@O

1 atom, 1 residue, 1 model selected  

> show #!4 models

> hide #!1 models

> select add #1

13182 atoms, 13112 bonds, 31 pseudobonds, 1050 residues, 8 models selected  

> select subtract #1

Nothing selected  

> select add #4

6591 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

363 atoms, 238 bonds, 125 residues, 1 model selected  

> select #4

6591 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

1 atom, 1 residue, 1 model selected  

> select sel @< 5

170 atoms, 130 bonds, 10 pseudobonds, 39 residues, 12 models selected  

> select clear

> select #1.1/B:30@ND1

1 atom, 1 residue, 1 model selected  

> select sel :< 5 & solvent

33 atoms, 21 bonds, 12 residues, 5 models selected  

> show sel & #!1.1-2 atoms

> select #1.1/B:358@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 2 models selected  

> select up

6 atoms, 4 bonds, 2 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #1.1/B:347@O

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 3 atom styles  

> select clear

> select #1.2/D:166@OH

1 atom, 1 residue, 1 model selected  

> hide #!1 models

> show #!4 models

> select #4/b:166

20 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:  
416 hydrogen bonds  
28 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:  
416 hydrogen bonds  
28 hydrogens added  
  

> show #!1 models

> select #1.2/D:166@HH

1 atom, 1 residue, 1 model selected  

> select #1.2@H*

28 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:  
870 hydrogen bonds  
56 hydrogens added  
  

> delete #5@H*

> ui mousemode right pivot

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right pivot

> select #5/D:166@CG

1 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

2 hydrogen bonds found  
2 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:  
867 hydrogen bonds  
56 hydrogens added  
  

> select #5/D:166@HH

1 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

1 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:  
850 hydrogen bonds  
1 hydrogens added  
  

> select #5/D:166@HH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> delete sel

> close #6

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select #5/B:30@NE2

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 atoms, 1 residue, 1 model selected  

> ~bond sel

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 1 pseudobond, 2 residues, 2 models selected  

> delete pbonds sel

> select clear

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 atoms, 1 residue, 1 model selected  

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> undo

[Repeated 2 time(s)]

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

1 hydrogen bonds found  
1 strict hydrogen bonds found  

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

1 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

1 atom, 1 residue, 1 model selected  

> select add #3/D:166@OH

2 atoms, 1 residue, 1 model selected  

> select add #3/B:540@D

3 atoms, 2 residues, 1 model selected  

> show #!5 models

> select #5/D:166@CZ

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 1 residue, 1 model selected  

> select add #5/B:30@HE2

3 atoms, 2 residues, 1 model selected  

> select #5/B:30@HE2

1 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

1 atom, 1 residue, 1 model selected  

> select #5/D:166@CD1

1 atom, 1 residue, 1 model selected  

> select #5/D:166@CD1

1 atom, 1 residue, 1 model selected  

> select #5/D:166@CD1

1 atom, 1 residue, 1 model selected  

> ui mousemode right pivot

> select #5/B:30@HE2

1 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 atoms, 2 residues, 1 model selected  

> ui tool show "Selection Inspector"

> select up

37 atoms, 37 bonds, 2 residues, 1 model selected  

> select add #5

13237 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

1 atom, 1 residue, 1 model selected  

> select up

3 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:  
849 hydrogen bonds  
1 hydrogens added  
  

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 2 residues, 1 model selected  

> select #5/B:30@HN

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 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:  
2 hydrogens added  
  

> select #5/D:166@CZ

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 1 residue, 1 model selected  

> select add #5/D:166@HH

3 atoms, 1 residue, 1 model selected  

> select #5/B:30@HE21

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> show #!6 models

> select #5/D:166@HH

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@HH

2 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

1 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

1 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

1 atom, 1 residue, 1 model selected  

> delete sel

> view y166-h30

> show #!6 models

> hide #!6 models

> select #5/D:166@CE1

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/d

3319 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

1 atom, 1 residue, 1 model selected  

> select sel :<5 & solvent

44 atoms, 29 bonds, 15 residues, 5 models selected  

> show sel & #!3 atoms

> select #3/D:335@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> view y166-h30

> select #3/D:327@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:336@D1

2 atoms, 2 residues, 1 model selected  

> select add #5/B:336@O

3 atoms, 2 residues, 1 model selected  

> select add #5/B:347@D2

4 atoms, 3 residues, 1 model selected  

> select add #5/B:347@D1

5 atoms, 3 residues, 1 model selected  

> select add #5/B:30@ND1

6 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

1 hydrogen bonds found  

> select add #5/B:336@O

3 atoms, 2 residues, 1 model selected  

> select add #5/B:347@D2

4 atoms, 3 residues, 1 model selected  

> select add #5/B:347@D1

5 atoms, 3 residues, 1 model selected  

> select add #5/B:30@ND1

6 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

1 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

1 hydrogen bonds found  

> select clear

> select #5/B:336@O

1 atom, 1 residue, 1 model selected  

> select add #5/B:347@D2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> show #5.3 models

> select clear

> delete pbonds sel

> select #5/B:30@ND1

1 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@ND1

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select up

2 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

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #5/B:161@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #5 & @@ display

626 atoms, 583 bonds, 26 pseudobonds, 53 residues, 5 models selected  

> select #5/b & @@ display

163 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

4 hydrogen bonds found  

> select clear

> select #5/B:327@O

1 atom, 1 residue, 1 model selected  

> select add #5/B:143@DE21

2 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

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #5/b & @@ display

162 atoms, 157 bonds, 14 pseudobonds, 13 residues, 5 models selected  

> select #5/b & @@ display & ~backbone

122 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

9 hydrogen bonds found  

> select #5/B:346@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:327@H1

2 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

746 atoms, 746 residues, 1 model selected  

> select #5 & main & @O

796 atoms, 796 residues, 1 model selected  

> select #5 & main & D

2 atoms, 2 residues, 1 model selected  

> select #5/B:163@DD1

1 atom, 1 residue, 1 model selected  

> select #5 & main & @D*

6128 atoms, 796 residues, 1 model selected  

> select add #5/B:30@HE2

6129 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

246 atoms, 41 residues, 1 model selected  

> select #5 & main & @D* & @@display & ~/a

178 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

133 atoms, 23 residues, 1 model selected  

> select up

391 atoms, 389 bonds, 23 residues, 1 model selected  

> select down

133 atoms, 23 residues, 1 model selected  

> select add #5/B:30@HE2

134 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

135 atoms, 1 bond, 23 residues, 1 model selected  

> select down

134 atoms, 1 bond, 23 residues, 1 model selected  

> select up

135 atoms, 1 bond, 23 residues, 1 model selected  

> select down

134 atoms, 1 bond, 23 residues, 1 model selected  

> select up

135 atoms, 1 bond, 23 residues, 1 model selected  

> select down

134 atoms, 1 bond, 23 residues, 1 model selected  

> select up

135 atoms, 1 bond, 23 residues, 1 model selected  

> select up

391 atoms, 389 bonds, 23 residues, 1 model selected  

> select down

135 atoms, 1 bond, 23 residues, 1 model selected  

> select down

134 atoms, 1 bond, 23 residues, 1 model selected  

> select up

391 atoms, 389 bonds, 23 residues, 1 model selected  

> select down

134 atoms, 23 residues, 1 model selected  

> select add #5/B:34@CD1

135 atoms, 23 residues, 1 model selected  

> select up

391 atoms, 389 bonds, 23 residues, 1 model selected  

> select down

135 atoms, 23 residues, 1 model selected  

> select subtract #5/B:34@CD1

134 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

1 atom, 1 bond, 1 residue, 1 model selected  

> select subtract #5/B:163@DD2

1 bond, 1 model selected  

> select add #5/B:163@DD2

1 atom, 1 bond, 1 residue, 1 model selected  

> select subtract #5/B:163@DD2

1 bond, 1 model selected  

> select up

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

> select down

3 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

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add #5/B:163@ND1

2 atoms, 3 bonds, 2 residues, 1 model selected  

> select subtract #5/B:163@ND1

1 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

6 bonds, 1 model selected  

> size =sel stickRadius 0.12

Changed 7 bond radii  

> select add #5/B:30@DD2

1 atom, 14 bonds, 1 residue, 1 model selected  

> select subtract #5/B:30@DD2

14 bonds, 1 model selected  

> select add #5/B:30@DD2

1 atom, 14 bonds, 1 residue, 1 model selected  

> select add #5/D:166@DE2

2 atoms, 16 bonds, 2 residues, 1 model selected  

> select subtract #5/D:166@DE2

1 atom, 16 bonds, 1 residue, 1 model selected  

> select add #5/D:166@DE2

2 atoms, 16 bonds, 2 residues, 1 model selected  

> select subtract #5/D:166@DE2

1 atom, 16 bonds, 1 residue, 1 model selected  

> select add #5/D:166@DE2

2 atoms, 17 bonds, 2 residues, 1 model selected  

> select subtract #5/D:166@DE2

1 atom, 17 bonds, 1 residue, 1 model selected  

> size =sel stickRadius 0.12

Changed 19 bond radii  

> select subtract #5/B:30@DD2

19 bonds, 1 model selected  

> select add #5/B:30@DD2

1 atom, 19 bonds, 1 residue, 1 model selected  

> select subtract #5/B:30@DD2

19 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

1 atom, 1 bond, 1 residue, 1 model selected  

> select clear

> select #5/b,d & main & @D* & @@display

133 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

133 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

20 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

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #5/B:76

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #5/B:77

20 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

15 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

1 atom, 1 residue, 1 model selected  

> select up

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

> select sel & ~sidechain

4 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select #5/D:171

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select add #5/D:170

36 atoms, 34 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select #5/B:161@N

1 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

133 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

1 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:34@OH

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:161@D

2 atoms, 2 residues, 1 model selected  

> select up

38 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

1 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

22 atoms, 6 bonds, 1 pseudobond, 16 residues, 2 models selected  

> select #3/b,d & @@display & sideonly

116 atoms, 114 bonds, 5 pseudobonds, 11 residues, 3 models selected  

> select #3/b,d & @@display & ~backbone

124 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

11 hydrogen bonds found  

> select #3/D:306@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #3/B:163@DA

1 atom, 1 residue, 1 model selected  

> select #3/B:163@CG

1 atom, 1 residue, 1 model selected  

> delete pbonds sel

[Repeated 1 time(s)]

> select clear

> select #3/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/B:161@O

1 atom, 1 residue, 1 model selected  

> select add #3/B:161@DA

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

> hide sel atoms

> select clear

> select #3/B:163@O

1 atom, 1 residue, 1 model selected  

> select add #3/B:163@DA

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/D:335@O

2 atoms, 2 residues, 1 model selected  

> select #3/D:335@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #3/B:163@D

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

> select add #3/B:163@N

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

> hide sel atoms

> select clear

> select #3/B:142@O

1 atom, 1 residue, 1 model selected  

> select #3/B:142

14 atoms, 13 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #3/B:30@C

1 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

1 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@C

2 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #3/B:70

7 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

15 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:123@DE1

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select #3/B:143@DE22

1 atom, 1 residue, 1 model selected  

> select add #3/B:34@OH

2 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

393 atoms, 70 residues, 6 models selected  

> select /b,d & main & @D* & @@display & ##display

237 atoms, 41 residues, 4 models selected  

> select clear

> select /b,d & main & @D* & @@display & ##display

237 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

237 atoms, 41 residues, 4 models selected  

> help help:user

> select #3 & /b,d & main & @D* & @@display

61 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

61 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

61 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

61 atoms, 61 bonds, 11 residues, 1 model selected  

> select add #3/B:566@D

62 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:34@OH

2 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

0 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

1 atom, 1 residue, 1 model selected  

> select #3/B:34@OH

1 atom, 1 residue, 1 model selected  

> select add #3/B:143@DE22

2 atoms, 2 residues, 1 model selected  

> show #3.4 models

> select add #3.5

2 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

3 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1.1/A:123@DE3

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select #1.1/A:66@DZ

1 atom, 1 residue, 1 model selected  

> select up

20 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

14 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 atoms, 2 residues, 1 model selected  

> select add #5/B:30@NE2

3 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:143@DE22

2 atoms, 2 residues, 1 model selected  

> select add #3/B:143@NE2

3 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

3 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

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #3/B:30

17 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

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #5/B:161@N

1 atom, 1 residue, 1 model selected  

> select add #5/B:161@D

2 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

11 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

2 pseudobonds, 3 models selected  

> select add #5

13235 atoms, 13165 bonds, 32 pseudobonds, 1050 residues, 6 models selected  

> select subtract #5

1 model selected  

> select add #4

1 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

17 atoms, 16 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #5/B:30

17 atoms, 16 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select add #5.3.1

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  
  
434 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add sel @< 10

409 atoms, 372 bonds, 57 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select sel @< 5

47 atoms, 37 bonds, 12 residues, 1 model selected  

> show sel atoms

> select up

178 atoms, 176 bonds, 12 residues, 1 model selected  

> show sel atoms

> select /A:71

17 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

1 atom, 1 residue, 1 model selected  

> select /A:163@NE2

1 atom, 1 residue, 1 model selected  

> select add /D:4@FE

2 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

372 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*

2674 atoms, 396 residues, 1 model selected  

> hide sel atoms

> select clear

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> view sel

> ui tool show H-Bonds

> hbonds reveal true

2448 hydrogen bonds found  

> undo

> redo

> ~hbonds

> hbonds sel reveal true

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel reveal true

0 hydrogen bonds found  

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select sel @< 5

47 atoms, 37 bonds, 12 residues, 1 model selected  

> select up

168 atoms, 166 bonds, 12 residues, 1 model selected  

> select ~sel

6368 atoms, 5742 bonds, 1086 residues, 1 model selected  

> hide sel atoms

> select ~sel & ##selected

168 atoms, 184 bonds, 12 residues, 1 model selected  

> select @H*

2674 atoms, 396 residues, 1 model selected  

> hide sel atoms

> select clear

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true

2 hydrogen bonds found  

> select @H*

2674 atoms, 396 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true

2 hydrogen bonds found  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select /A:163@NE2

1 atom, 1 residue, 1 model selected  

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:163@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:26@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:74@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /A:159@OD2

2 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

1 atom, 1 residue, 1 model selected  

> select /A:123@NE1

1 atom, 1 residue, 1 model selected  

> select add /A:143@CD

2 atoms, 2 residues, 1 model selected  

> select up

23 atoms, 23 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 restrict both reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select /A:34@CZ

1 atom, 1 residue, 1 model selected  

> select /A:34@OH

1 atom, 1 residue, 1 model selected  

> select add /A:30@ND1

2 atoms, 2 residues, 1 model selected  

> select add /A:30@NE2

3 atoms, 2 residues, 1 model selected  

> select add /A:163@ND1

4 atoms, 3 residues, 1 model selected  

> select add /A:26@ND1

5 atoms, 4 residues, 1 model selected  

> select add /A:74@ND1

6 atoms, 5 residues, 1 model selected  

> select add /A:159@OD1

7 atoms, 6 residues, 1 model selected  

> select add /A:161@NE1

8 atoms, 7 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

11 hydrogen bonds found  

> select clear

> select /S:229@O

1 atom, 1 residue, 1 model selected  

> select add /S:12@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> hide sel

> select clear

> hide sel

> select clear

> select /D:4@FE

1 atom, 1 residue, 1 model selected  

> select add /E:2@O

2 atoms, 2 residues, 1 model selected  

> hbonds sel

2 hydrogen bonds found  

> undo

> select /A:143@NE2

1 atom, 1 residue, 1 model selected  

> select add /S:263@O

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

9 hydrogen bonds found  

> select /S:229@O

1 atom, 1 residue, 1 model selected  

> select add /S:110@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select /A:143@OE1

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

2 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

1 atom, 1 residue, 1 model selected  

> select add /E:2@O

2 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

9 atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract /A:187

2 pseudobonds, 1 model selected  

> select add /A:187

9 atoms, 8 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract /A:187

3 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

1 atom, 1 residue, 1 model selected  

> view sel

> cofr sel

> select clear

> select /A:161@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select clear

> select /E:2@O

1 atom, 1 residue, 1 model selected  

> select add /S:263@O

2 atoms, 2 residues, 1 model selected  

> style sel ball

Changed 2 atom styles  

> select clear

> help help:user

> surface cap true

> select /A:120

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

> select add /A:121

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

> select add /A:122

14 atoms, 11 bonds, 3 residues, 1 model selected  

> select add /A:123

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select subtract /A:123

14 atoms, 11 bonds, 3 residues, 1 model selected  

> select add /A:141

21 atoms, 18 bonds, 4 residues, 1 model selected  

> select subtract /A:141

14 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

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

> select /A:163

10 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

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.4.1

1 model selected  

> select subtract #1.4.1

Nothing selected  

> select add #1.4.2

1 model selected  

> select subtract #1.4.2

Nothing selected  

> select add #1.3.1

1 model selected  

> select add #1.3.2

2 models selected  

> select subtract #1.3.2

1 model selected  

> select add #1.3.2

2 models selected  

> select subtract #1.3.1

1 model selected  

> select subtract #1.3.2

Nothing selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 3 models selected  

> hide #1.3.1 models

> show #1.3.1 models

> select subtract #1.3.1

1574 atoms, 198 residues, 3 models selected  

> select add #1.3.1

1574 atoms, 198 residues, 4 models selected  

> select subtract #1.3

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> select add #1.4

1574 atoms, 198 residues, 3 models selected  

> select subtract #1.4

1 model selected  

> hide #!1.4 target m

> hide #!1.3 models

> show #1.3 models

> select add #1.3

1574 atoms, 198 residues, 1 model selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 atoms, 198 residues, 1 model selected  

> select subtract #1.3

1 model selected  

> select add #1.3

1574 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  
  
7kks 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  
  
7kks mmCIF Assemblies  
---  
1| 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:
0.393)  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select clear

> select #2/B:161@CG

1 atom, 1 residue, 1 model selected  

> select up

24 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

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@NE2

2 atoms, 2 residues, 1 model selected  

> select up

19 atoms, 17 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

12 hydrogen bonds found  

> select #2/B:73@ND2

1 atom, 1 residue, 1 model selected  

> select up

14 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #2/B:30

36 atoms, 36 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #2/B:34@OH

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

5 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

3863 atoms, 3252 bonds, 17 pseudobonds, 1099 residues, 4 models selected  

> select subtract #1

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

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@DE22

2 atoms, 2 residues, 1 model selected  

> select clear

> show #!1 models

> hide #!1 models

> select add #2/B:74@NE2

1 atom, 4 pseudobonds, 1 residue, 2 models selected  

> select clear

> select #2/B:201@MN

1 atom, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> select up

3305 atoms, 3284 bonds, 266 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select add #2/B:74@NE2

1 atom, 2 pseudobonds, 1 residue, 2 models selected  

> select subtract #2/B:74@NE2

2 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

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

> hide sel cartoons

> select clear

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #2/B:160

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select add #2/B:162

55 atoms, 54 bonds, 3 residues, 1 model selected  

> select add #2/B:163

72 atoms, 71 bonds, 4 residues, 1 model selected  

> select clear

> select #2/B:162

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

> select add #2/B:161

39 atoms, 39 bonds, 2 residues, 1 model selected  

> select subtract #2/B:161

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

> select add #2/B:161

39 atoms, 39 bonds, 2 residues, 1 model selected  

> select add #2/B:160

55 atoms, 54 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #2/B:121

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

> hide sel

> hide sel cartoons

> select clear

> select #2/B:162

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

> show sel cartoons

> select #2/B:161-150

Nothing selected  

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select #2/B:160

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

> show sel atoms

> select #2/B:160

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

> hide sel atoms

> show sel cartoons

> select clear

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #2/B:160

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select add #2/B:141

54 atoms, 54 bonds, 3 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #2/B:327@O

1 atom, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 2 atom styles  

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select up

3 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:
0.000)  
  

> 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/B:161

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4.2/B:162

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

> show sel atoms

> select #4.2/B:166@CZ

1 atom, 1 residue, 1 model selected  

> select add #4.2/B:162@CD

2 atoms, 2 residues, 1 model selected  

> select add #2/B:163@ND1

3 atoms, 1 bond, 3 residues, 2 models selected  

> select up

5 atoms, 1 bond, 4 residues, 2 models selected  

> select up

68 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

4 hydrogen bonds found  

> select #4.2/B:120

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

> select #4.2/B:119

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #4.2/B:120

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

> select add #4.2/B:121

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select add #4.2/B:119

35 atoms, 32 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #2/B:201@MN

1 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

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/B:201@MN

1 atom, 1 residue, 1 model selected  

> hide sel

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

3 hydrogen bonds found  

> select clear

> select #2/B:34@CZ

1 atom, 1 residue, 1 model selected  

> select #2/B:143@DE22

1 atom, 1 residue, 1 model selected  

> select #2/B:34@OH

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@DE22

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 restrict both reveal true retainCurrent
> true

0 hydrogen bonds found  

> select clear

> select #2/B:201@MN

1 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/B:123@CD1

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/B:74@CE1

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

34 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

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select add #2/B:327@O

2 atoms, 2 residues, 1 model selected  

> select up

5 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

6591 atoms, 6556 bonds, 10 pseudobonds, 525 residues, 2 models selected  

> color (#!4.2 & sel) byhetero

> select subtract #4.2

Nothing selected  

> select add #3

23 pseudobonds, 1 model selected  

> color #3 #ff40ffff models

> select clear

> select #2/B:201@MN

1 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

1 model selected  

> ui tool show "Selection Inspector"

> select subtract #2.3

Nothing selected  

> select add #2.3

1 model selected  
No visible atoms selected  

> select clear

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 2"

> select #2/B:327@O

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text "WAT 1"

> label sel text WAT1

> select #2/B:336@O

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text WAT2

> select #2/B:201@MN

1 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

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #2/B:68

20 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

6591 atoms, 6556 bonds, 16 pseudobonds, 525 residues, 4 models selected  

> select add #4

13182 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

1 atom, 2 bonds, 1 residue, 2 models selected  

> select add #2/B:163@DB2

2 atoms, 2 bonds, 2 residues, 2 models selected  

> select add #2/B:163@CE1

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

> select add #2/B:336@O

4 atoms, 5 bonds, 3 residues, 2 models selected  

> select add #2/B:327@O

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

> select add #2/B:123@CZ2

6 atoms, 6 bonds, 5 residues, 2 models selected  

> select add #2/B:143@CG

7 atoms, 6 bonds, 6 residues, 2 models selected  

> select add #2/B:73@CB

8 atoms, 6 bonds, 7 residues, 2 models selected  

> select up

20 atoms, 6 bonds, 13 residues, 2 models selected  

> select up

201 atoms, 197 bonds, 13 residues, 2 models selected  

> select up

203 atoms, 198 bonds, 14 residues, 2 models selected  

> select up

218 atoms, 215 bonds, 14 residues, 2 models selected  

> select add #2/B:201@MN

219 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

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

> select up

35 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 2"

> select up

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

> label sel text "WAT 2"

> label sel text "WAT 1"

> select #2/B:201@MN

1 atom, 1 residue, 1 model selected  

> label sel text Mn

> select clear

> select #2/B:142

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select add #2/B:143

31 atoms, 29 bonds, 2 residues, 1 model selected  

> select add #2/B:144

43 atoms, 40 bonds, 3 residues, 1 model selected  

> help help:user

> select clear

> select #2/B:143

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select down

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2/B:142

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/B:144

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #2/B:142

26 atoms, 24 bonds, 2 residues, 1 model selected  

> select add #2/B:143

43 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

1 atom, 1 residue, 1 model selected  

> select up

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

> select #2/B:327@D2

1 atom, 1 residue, 1 model selected  

> select #2/B:159@OD1

1 atom, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ff40ff dashes 6 reveal true retainCurrent true

2 hydrogen bonds found  

> select clear

> select #2/B:161

24 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

1 atom, 1 residue, 1 model selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@N

2 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

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@C

2 atoms, 1 residue, 1 model selected  

> select add #2/B:161@CA

3 atoms, 1 residue, 1 model selected  

> select add #2/B:161@DA

4 atoms, 1 residue, 1 model selected  

> select subtract #2/B:161@CA

3 atoms, 1 residue, 1 model selected  

> select add #2/B:161@CA

4 atoms, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/B:143

17 atoms, 16 bonds, 1 residue, 1 model selected  

> ribbon sel suppressBackboneDisplay false

> select #2/B:143@D

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@N

2 atoms, 1 residue, 1 model selected  

> select subtract #2/B:143

Nothing selected  

> select #2/B:143

17 atoms, 16 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #2/B:143@C

1 atom, 1 residue, 1 model selected  

> select #2/B:143@CA

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@D

2 atoms, 1 residue, 1 model selected  

> select add #2/B:143@N

3 atoms, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> show sel atoms

> select #2/B:143@D

1 atom, 1 residue, 1 model selected  

> select add #2/B:143@N

2 atoms, 1 residue, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select #2/B:143@C

1 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

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel atoms

> select #2/B:161@DA

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@C

2 atoms, 1 residue, 1 model selected  

> select add #2/B:161@O

3 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

1 atom, 1 residue, 1 model selected  

> select up

24 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select subtract #2/B:161

Nothing selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select add #2/B:161@D

1 atom, 1 pseudobond, 1 residue, 2 models selected  

> select clear

> select #2/B:161@D

1 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

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

> select #2/B:162

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

> select #2/B:161@CA

1 atom, 1 residue, 1 model selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> select #2/B:161@N

1 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

24 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

1 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

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select add #2/B:142

31 atoms, 29 bonds, 2 residues, 1 model selected  

> select subtract #2/B:143

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/B:143

17 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

31 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2/B:161@D

1 atom, 1 residue, 1 model selected  

> select #2/B:161@CB

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select #2/B:161@O

1 atom, 1 residue, 1 model selected  

> select add #2/B:161@C

2 atoms, 1 residue, 1 model selected  

> select add #2/B:161@DA

3 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select #2/B:180

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2/B:161@N

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2/B:161@N

1 atom, 1 residue, 1 model selected  

> select #2/B:161@CB

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select subtract #2/B:161@D

23 atoms, 24 bonds, 1 residue, 1 model selected  

> select subtract #2/B:161@N

22 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

1 atom, 1 residue, 1 model selected  

> select add #2/B:336@O

2 atoms, 2 residues, 1 model selected  

> select add #2/B:327@O

3 atoms, 3 residues, 1 model selected  

> select up

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

> select ~sel & ##selected

6585 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

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

> select up

17 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label sel bgColor white

> select up

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

> select up

12 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

1 atom, 1 residue, 1 model selected  

> select up

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

> select down

1 atom, 1 residue, 1 model selected  

> select up

2 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

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel height 0.65

> select clear

> select #2/B:144

12 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

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

> select up

12 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

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel bgColor white

> select clear

> color #3 #00fdffff models

> select clear

> select add #4.2

6591 atoms, 6556 bonds, 10 pseudobonds, 525 residues, 3 models selected  

> select add #2

13182 atoms, 13112 bonds, 27 pseudobonds, 1050 residues, 7 models selected  

> color sel #F187EE

> color sel byhetero

> select subtract #2

6591 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

1 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

1 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

1 atom, 1 residue, 1 model selected  

> label sel text Mn(III)

> select #2/B:143@CD

1 atom, 1 residue, 1 model selected  

> select up

17 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

3305 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

1 atom, 1 residue, 1 model selected  

> select add #4.2/D:162@DG2

2 atoms, 2 residues, 1 model selected  

> select up

35 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> label sel offset 0,0,5

> select #2/B:74@ND1

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> label sel offset 0,0,5

> select #2/B:327@O

1 atom, 1 residue, 1 model selected  

> select up

2 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  
---  
1| 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:
0.320)  
  

> select #1 & @@display

482 atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected  

> select #2 & #1 :<1

12662 atoms, 12752 bonds, 20 pseudobonds, 890 residues, 4 models selected  

> select #1 & @@display

482 atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected  

> select #2 & sel :<1

623 atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected  

> show sel atoms

> name frozen sh-r sel

> select #1 & @@display

482 atoms, 466 bonds, 30 pseudobonds, 44 residues, 5 models selected  

> name frozen sh-o sel

> select sh-r

623 atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected  

> select sh-r

623 atoms, 608 bonds, 20 pseudobonds, 48 residues, 4 models selected  

> hide #!1 models

> select add #2.1/A:302@O

624 atoms, 608 bonds, 20 pseudobonds, 49 residues, 4 models selected  

> select up

626 atoms, 610 bonds, 20 pseudobonds, 49 residues, 4 models selected  

> select add #2.1/A:541@D

627 atoms, 610 bonds, 20 pseudobonds, 50 residues, 4 models selected  

> name frozen sh-r sel

> select #2.1/A:324@D1

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> select #2.1/A:25

19 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

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2.1/A:161

24 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

417 atoms, 394 bonds, 20 pseudobonds, 50 residues, 4 models selected  

> hbonds sel restrict #2 reveal true interSubmodel true name red_hbonds

52 hydrogen bonds found  

> select #2.1/A:162

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

> select #2.2/A:162

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

> select add #2.2/A:166

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select ~sel & ##selected

6521 atoms, 6489 bonds, 32 pseudobonds, 521 residues, 3 models selected  

> hide sel atoms

> select #2.1/A:166

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #2.1/A:162

35 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2.1/A:338@O

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:326@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select up

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

> select up

3 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

49 atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected  

> select #2.1/A:201@MN

1 atom, 1 residue, 1 model selected  

> select #2 & pbondatoms & @@display

49 atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected  

> select clear

> select add #3

52 pseudobonds, 1 model selected  

> select up

52 pseudobonds, 3 models selected  

> select up

52 pseudobonds, 3 models selected  

> select up

52 pseudobonds, 3 models selected  

> select up

52 pseudobonds, 3 models selected  

> select down

52 pseudobonds, 1 model selected  

> select down

52 pseudobonds, 1 model selected  

> select clear

> select #2 & pbondatoms & @@display

49 atoms, 1 bond, 31 pseudobonds, 31 residues, 4 models selected  

> select subtract #2.1/A:201@MN

48 atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected  

> select subtract #2.1/A:26@NE2

47 atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected  

> select subtract #2.1/A:163@NE2

46 atoms, 1 bond, 26 pseudobonds, 30 residues, 4 models selected  

> select subtract #2.1/A:317@O

45 atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected  

> select subtract #2.1/A:74@NE2

44 atoms, 1 bond, 26 pseudobonds, 29 residues, 4 models selected  

> select subtract #2.1/A:30@NE2

43 atoms, 1 bond, 24 pseudobonds, 28 residues, 4 models selected  

> select subtract #2.2/A:166@OH

42 atoms, 1 bond, 23 pseudobonds, 27 residues, 4 models selected  

> select add #2.2/A:166@OH

43 atoms, 1 bond, 23 pseudobonds, 28 residues, 4 models selected  

> hbonds sel restrict both reveal true interSubmodel true name red_hbonds

5 hydrogen bonds found  

> select up

410 atoms, 404 bonds, 5 pseudobonds, 28 residues, 3 models selected  

> hbonds sel restrict both interSubmodel true name red_hbonds

22 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:501@D

2 atoms, 2 residues, 1 model selected  

> pbond sel dashes 0 name shared-H

> select subtract #2.1/A:501@D

1 atom, 1 residue, 1 model selected  

> select #2.1/A:501@D

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:143@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel dashes 0 name shared-H

> select #2.1/A:30@NE2

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:541@D

2 atoms, 2 residues, 1 model selected  

> pbond sel dashes 0 name shared-H

> select #2.1/A:541@D

1 atom, 1 residue, 1 model selected  

> select add #2.2/A:166@OH

2 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

2 atoms, 3 pseudobonds, 2 residues, 3 models selected  

> select add #3

2 atoms, 4 pseudobonds, 2 residues, 4 models selected  

> select add #2.1

6557 atoms, 6523 bonds, 33 pseudobonds, 524 residues, 6 models selected  

> select subtract #2.1

1 atom, 1 residue, 1 model selected  

> select add #2.2

6556 atoms, 6523 bonds, 12 pseudobonds, 523 residues, 3 models selected  

> select subtract #2.2

Nothing selected  

> select add #2.1.2

3 pseudobonds, 1 model selected  

> select add #3

4 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

3 pseudobonds, 1 model selected  

> select add #2.1.2.1

4 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

12 atoms, 3 pseudobonds, 12 residues, 3 models selected  

> select up

192 atoms, 189 bonds, 3 pseudobonds, 12 residues, 3 models selected  

> select down

12 atoms, 3 pseudobonds, 12 residues, 3 models selected  

> select #2 & sel @<1

12 atoms, 3 pseudobonds, 12 residues, 3 models selected  

> select #2 & sel @<1.5

24 atoms, 12 bonds, 3 pseudobonds, 12 residues, 3 models selected  

> select ~sel & ::selected & ~sidechain

24 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:70@DA2

2 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:143@C

2 atoms, 1 residue, 1 model selected  

> select add #2.1/A:163@D

3 atoms, 2 residues, 1 model selected  

> select add #2.1/A:163@N

4 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select #2.1/A:302@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

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

> select up

17 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

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2.1/A:28

33 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

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select clear

> select #2.1/A:501@D

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:317@O

2 atoms, 2 residues, 1 model selected  

> select add #2.1/A:330@O

3 atoms, 3 residues, 1 model selected  

> select add #2.1/A:541@D

4 atoms, 4 residues, 1 model selected  

> select up

7 atoms, 3 bonds, 4 residues, 1 model selected  

> style sel ball

Changed 7 atom styles  

> select clear

> select #2.1/A:541@D

1 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> select intersect sidechain

20 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

1 atom, 1 residue, 1 model selected  

> select up

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select & sidechain

Expected an objects specifier or a keyword  

> select sel & sidechain

13 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1.1/B:143@DA

1 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

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1.1/B:143@CB

1 atom, 1 residue, 1 model selected  

> show sel cartoons

> select #1.1/B:143@DA

1 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

8104 atoms, 6544 bonds, 1592 residues, 4 models selected  

> select C & @@display

358 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)

425 atoms, 84 residues, 4 models selected  

> hide sel & #!1.1-2 atoms

> select clear

> view active-site-1

> select @D* & ((C & @@display) @< 1.5)

425 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

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

> select up

12 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

778 atoms, 659 bonds, 51 pseudobonds, 97 residues, 11 models selected  

> select #2:* & @@display & ~backbone

352 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

84 atoms, 22 bonds, 17 residues, 1 model selected  

> ~label sel residues

> select #2.2/A:166@CD1

1 atom, 1 residue, 1 model selected  

> select add #2.2/A:162@CG

2 atoms, 2 residues, 1 model selected  

> select up

35 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

3267 atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected  

> select add #2.2

6556 atoms, 6523 bonds, 12 pseudobonds, 523 residues, 4 models selected  

> select #2.2/a

3267 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

3267 atoms, 3251 bonds, 7 pseudobonds, 261 residues, 3 models selected  

> select #2.2/D:162@CG

1 atom, 1 residue, 1 model selected  

> select add #2.2/D:166@CE1

2 atoms, 2 residues, 1 model selected  

> select up

35 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

1 atom, 1 residue, 1 model selected  

> select add #2.1/A:501@D

2 atoms, 2 residues, 1 model selected  

> ~label sel residues

> select #2.1/A:330@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 2"

> select #2.1/A:317@D1

1 atom, 1 residue, 1 model selected  

> select up

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

> label sel text "WAT 1"

> label sel height 0.6

> select #2.1/A:201@MN

1 atom, 1 residue, 1 model selected  

> select up

3267 atoms, 3251 bonds, 261 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> label sel text Mn(II)

> show #!1 models

> hide #!1 models

> select #2.1/A:330@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

2 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

1 atom, 1 residue, 1 model selected  

> select up

16 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

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

> select up

17 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

1 atom, 1 residue, 1 model selected  

> select add #1.1/B:143@C

2 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

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2.1/A:166

41 atoms, 41 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select clear

> view name active-site_red

> select #2.1/A:162

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

> select up

66 atoms, 68 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select up

3107 atoms, 3153 bonds, 199 residues, 1 model selected  

> show sel cartoons

> select clear

> select #2.1/A:74@CG

1 atom, 1 residue, 1 model selected  

> select up

17 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

1 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

1 atom, 1 residue, 1 model selected  

> label sel height 0.7

> select clear

[Repeated 2 time(s)]

> select #2.1/A:180

19 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> view sel

> view active-site-3

> select add #2.1/A:22

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select clear

> select #2.1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]

> select add #2.1.2

4 pseudobonds, 2 models selected  

> style sel dashes 12

Changed 2 pseudobond dashes  

> select clear

> view active-site-3

> select add #2.1.1

11 pseudobonds, 1 model selected  

> select subtract #2.1.1

Nothing selected  

> select add #2.1.2

4 pseudobonds, 2 models selected  

> style sel dashes 10

Changed 2 pseudobond dashes  

> select clear

> select add #2.1.2

4 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

13112 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

13112 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

19668 atoms, 19569 bonds, 58 pseudobonds, 1569 residues, 9 models selected  

> select subtract #2.1

13112 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

22 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

6556 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:
0.292)  
  

> 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

1 atom, 1 residue, 1 model selected  

> cofr sel

> select #3/B:34@OH

1 atom, 1 residue, 1 model selected  

> select add #3/B:566@D

2 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

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #3/D:162

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select up

186 atoms, 191 bonds, 10 residues, 1 model selected  

> select up

3114 atoms, 3160 bonds, 199 residues, 1 model selected  

> select subtract #3/D:162

3099 atoms, 3144 bonds, 198 residues, 1 model selected  

> select subtract #3/D:166

3079 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

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

181 atoms, 184 bonds, 10 residues, 1 model selected  

> show sel cartoons

> select clear

> hbonds #3 & @@display restrict both interModel false name red_hbonds

11 hydrogen bonds found  

> delete sel

> ~bond sel

> delete pbonds sel

[Repeated 1 time(s)]

> select clear

> select add #3/B:143@NE2

1 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:143@NE2

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:540@D

2 atoms, 2 residues, 1 model selected  

> pbond sel name shared-H

> select #3/B:30@NE2

1 atom, 1 residue, 1 model selected  

> select #3/B:540@D

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel name shared-H

> select add #3.2

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

2 atoms, 24 pseudobonds, 2 residues, 3 models selected  

> select subtract #3.1

2 atoms, 2 pseudobonds, 2 residues, 2 models selected  

> select add #3.1

2 atoms, 24 pseudobonds, 2 residues, 3 models selected  

> select subtract #3.2

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

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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> label sel text "WAT 1"

> select #3/B:348@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 3 atom styles  

> select #3/B:201@MN

1 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

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[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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[Repeated 3 time(s)]

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> color sel #be95f2ff

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[Repeated 1 time(s)]

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[Repeated 3 time(s)]

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[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

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> 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)]

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[Repeated 3 time(s)]

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[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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> color sel #ffe0f0ff

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[Repeated 1 time(s)]

> color sel #ffe2f0ff

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> color sel #ffe3f1ff

[Repeated 2 time(s)]

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[Repeated 1 time(s)]

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[Repeated 1 time(s)]

> color sel #ffe2f1ff

> color sel #ffe0f0ff

> color sel #ffdbedff

> color sel #ffd9ecff

[Repeated 1 time(s)]

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> color sel #ffd4eaff

> color sel #ffd4e9ff

> color sel #ffd2e8ff

> color sel #ffd0e7ff

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[Repeated 3 time(s)]

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[Repeated 1 time(s)]

> color sel #ffcbe5ff

> color sel #ffc5e2ff

> color sel #ffb6dbff

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[Repeated 3 time(s)]

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> color sel #ffb3d9ff

> color sel #ffb2d8ff

> color sel #ffb1d8ff

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> color sel #ffadd6ff

> color sel #ffacd6ff

> color sel #ffacd5ff

> color sel #ffacd6ff

> color sel #ffadd6ff

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> 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

13112 atoms, 13046 bonds, 48 pseudobonds, 1046 residues, 10 models selected  

> select subtract #2

Nothing selected  

> select add #2

13112 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

3289 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

6556 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

6556 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

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> color sel cadet blue target acsf

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> color sel medium spring green target acsf

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> color sel rebecca purple target acsf

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> color sel dark violet target acsf

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> 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:201@MN

2 atoms, 2 residues, 1 model selected  

> ~bond sel

> delete bonds sel

> select #3/B:201@MN

1 atom, 1 residue, 1 model selected  

> select add #3/B:319@O

2 atoms, 2 residues, 1 model selected  

> delete bonds sel

> select clear

> select #3/B:143@DG3

1 atom, 1 residue, 1 model selected  

> select add #3/B:143@DB3

2 atoms, 1 residue, 1 model selected  

> bond sel

Created 0 bonds  

> select #3/B:143@DE22

1 atom, 1 residue, 1 model selected  

> select add #3/B:34@OH

2 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

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

> select clear

> select #3/B:74@NE2

1 atom, 1 residue, 1 model selected  

> select add #3/B:74@CE1

2 atoms, 1 residue, 1 model selected  

> select #3/B:30@DB3

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@CB

2 atoms, 1 residue, 1 model selected  

> select #3/B:348@O

1 atom, 1 residue, 1 model selected  

> select add #3/B:348@D2

2 atoms, 1 residue, 1 model selected  

> ~bond sel

> bond sel

Created 1 bond  

> select #3/B:30@DD1

1 atom, 1 residue, 1 model selected  

> select add #3/B:30@DB3

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:201@MN

2 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

1 atom, 1 residue, 1 model selected  

> select add #3/B:201@MN

2 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/B:73@CB

1 atom, 1 residue, 1 model selected  

> select up

14 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

2 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

1 atom, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1.1/B:73@CB

1 atom, 1 residue, 1 model selected  

> select #1.1/B:73@CB

1 atom, 1 residue, 1 model selected  

> select up

14 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

1 atom, 1 residue, 1 model selected  

> select sel @< 5

157 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

392 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

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select up

120 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  
  
7kks 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  
  
7kks mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select #4:166

40 atoms, 40 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #4:166

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select sel @< 5 & ~sel

1264 atoms, 1113 bonds, 166 residues, 6 models selected  

> show sel & #!4 atoms

> select up

2552 atoms, 2534 bonds, 166 residues, 6 models selected  

> show sel & #!4 atoms

> hide sel & #!4 atoms

> select clear

> select #4/B:327@O

1 atom, 1 residue, 1 model selected  

> hide #!4 models

> view y166-h30

> show #!3 models

> select #3/B:540@D

1 atom, 1 residue, 1 model selected  

> select up

3289 atoms, 3273 bonds, 262 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select clear

> select #4:his

339 atoms, 343 bonds, 20 residues, 1 model selected  

> select #3:his

680 atoms, 688 bonds, 40 residues, 1 model selected  

> select #3:D

Nothing selected  

> select #3:D8U

8 atoms, 8 residues, 1 model selected  

> select #1:D8U

Nothing selected  

> select #2:D8U

8 atoms, 8 residues, 2 models selected  

> select #4:D8U

Nothing selected  

> select #4@D8U

Nothing selected  

> select #4@D

373 atoms, 373 residues, 1 model selected  

> select #2@D

752 atoms, 752 residues, 2 models selected  

> select #2.1@D

376 atoms, 376 residues, 1 model selected  

> select #3@D

752 atoms, 752 residues, 1 model selected  

> select #3@D

752 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

373 atoms, 373 residues, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> ui tool show "Selection Inspector"

> select up

5865 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

373 atoms, 373 residues, 1 model selected  

> select #4@D*

3302 atoms, 518 residues, 1 model selected  

> show sel atoms

> select up

6584 atoms, 6556 bonds, 518 residues, 1 model selected  

> show sel atoms

> show #4 atoms

> select clear

> select #4/A:306@O

1 atom, 1 residue, 1 model selected  

> select up

3286 atoms, 3272 bonds, 259 residues, 1 model selected  

> select down

1 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

1 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

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show sel atoms

> view y166-h30

> select #1.1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1.1/A:30@DD1

1 atom, 1 residue, 1 model selected  

> select sel @< 5

178 atoms, 133 bonds, 1 pseudobond, 44 residues, 7 models selected  

> select sel & solvent

33 atoms, 20 bonds, 13 residues, 6 models selected  

> show sel & #!1.1-2 atoms

> select #1.1/A:306@O

1 atom, 1 residue, 1 model selected  

> select up

3286 atoms, 3272 bonds, 259 residues, 1 model selected  

> select #1.1/A:306@O

1 atom, 1 residue, 1 model selected  

> show #!4 models

> hide #!1 models

> select add #1

13182 atoms, 13112 bonds, 31 pseudobonds, 1050 residues, 8 models selected  

> select subtract #1

Nothing selected  

> select add #4

6591 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

363 atoms, 238 bonds, 125 residues, 1 model selected  

> select #4

6591 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

1 atom, 1 residue, 1 model selected  

> select sel @< 5

170 atoms, 130 bonds, 10 pseudobonds, 39 residues, 12 models selected  

> select clear

> select #1.1/B:30@ND1

1 atom, 1 residue, 1 model selected  

> select sel :< 5 & solvent

33 atoms, 21 bonds, 12 residues, 5 models selected  

> show sel & #!1.1-2 atoms

> select #1.1/B:358@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 2 models selected  

> select up

6 atoms, 4 bonds, 2 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #1.1/B:347@O

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 3 atom styles  

> select clear

> select #1.2/D:166@OH

1 atom, 1 residue, 1 model selected  

> hide #!1 models

> show #!4 models

> select #4/b:166

20 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:  
416 hydrogen bonds  
28 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:  
416 hydrogen bonds  
28 hydrogens added  
  

> show #!1 models

> select #1.2/D:166@HH

1 atom, 1 residue, 1 model selected  

> select #1.2@H*

28 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:  
870 hydrogen bonds  
56 hydrogens added  
  

> delete #5@H*

> ui mousemode right pivot

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right pivot

> select #5/D:166@CG

1 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

2 hydrogen bonds found  
2 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:  
867 hydrogen bonds  
56 hydrogens added  
  

> select #5/D:166@HH

1 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

1 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:  
850 hydrogen bonds  
1 hydrogens added  
  

> select #5/D:166@HH

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> delete sel

> close #6

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select #5/B:30@NE2

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 atoms, 1 residue, 1 model selected  

> ~bond sel

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 1 pseudobond, 2 residues, 2 models selected  

> delete pbonds sel

> select clear

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 atoms, 1 residue, 1 model selected  

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> undo

[Repeated 2 time(s)]

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

1 hydrogen bonds found  
1 strict hydrogen bonds found  

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 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

1 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

1 atom, 1 residue, 1 model selected  

> select add #3/D:166@OH

2 atoms, 1 residue, 1 model selected  

> select add #3/B:540@D

3 atoms, 2 residues, 1 model selected  

> show #!5 models

> select #5/D:166@CZ

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 1 residue, 1 model selected  

> select add #5/B:30@HE2

3 atoms, 2 residues, 1 model selected  

> select #5/B:30@HE2

1 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

1 atom, 1 residue, 1 model selected  

> select #5/D:166@CD1

1 atom, 1 residue, 1 model selected  

> select #5/D:166@CD1

1 atom, 1 residue, 1 model selected  

> select #5/D:166@CD1

1 atom, 1 residue, 1 model selected  

> ui mousemode right pivot

> select #5/B:30@HE2

1 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

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@NE2

2 atoms, 2 residues, 1 model selected  

> ui tool show "Selection Inspector"

> select up

37 atoms, 37 bonds, 2 residues, 1 model selected  

> select add #5

13237 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

1 atom, 1 residue, 1 model selected  

> select up

3 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:  
849 hydrogen bonds  
1 hydrogens added  
  

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 2 residues, 1 model selected  

> select #5/B:30@HN

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/D:166@OH

1 atom, 1 residue, 1 model selected  

> select add #5/B:30@HE2

2 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:  
2 hydrogens added  
  

> select #5/D:166@CZ

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 1 residue, 1 model selected  

> select add #5/D:166@HH

3 atoms, 1 residue, 1 model selected  

> select #5/B:30@HE21

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/B:30@HE2

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> show #!6 models

> select #5/D:166@HH

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@OH

2 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

1 atom, 1 residue, 1 model selected  

> select add #5/D:166@HH

2 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

1 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

1 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

1 atom, 1 residue, 1 model selected  

> delete sel

> view y166-h30

> show #!6 models

> hide #!6 models

> select #5/D:166@CE1

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/d

3319 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

1 atom, 1 residue, 1 model selected  

> select sel :<5 & solvent

44 atoms, 29 bonds, 15 residues, 5 models selected  

> show sel & #!3 atoms

> select #3/D:335@O

1 atom, 1 residue, 1 model selected  

> select up

3 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

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> view y166-h30

> select #3/D:327@O

1 atom, 1 residue, 1 model selected  

> select up

3 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 #!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 "Selection Inspector"

> open 8vhw

Summary of feedback from opening 8vhw 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  
  
8vhw title:  
Neutron Structure of Peroxide-Soaked Trp161Phe MnSOD [more info...]  
  
Chain information for 8vhw #4  
---  
Chain | Description | UniProt  
A B | Superoxide dismutase [Mn], mitochondrial | SODM_HUMAN 1-198  
  
Non-standard residues in 8vhw #4  
---  
MN — manganese (II) ion  
PEO — hydrogen peroxide  
  
306 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> 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 #!4 models

> select clear

> show #!4 models

> help help:user

> ui tool show Matchmaker

> matchmaker #4/B to #3/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain B (#3) with 8vhw, chain B (#4), sequence
alignment score = 1069.2  
RMSD between 199 pruned atom pairs is 0.337 angstroms; (across all 199 pairs:
0.337)  
  

> 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

> select #4/B:30

17 atoms, 17 bonds, 1 residue, 1 model selected  

> show sel atoms

> 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

> select #4/B:161@CB

1 atom, 1 residue, 1 model selected  

> select add #4/B:122

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select #4/B:161@CG

1 atom, 1 residue, 1 model selected  

> select clear

> select @@display

1950 atoms, 1769 bonds, 103 pseudobonds, 195 residues, 23 models selected  

> show sel & #!4 atoms

[Repeated 1 time(s)]

> hide sel & #!4 atoms

> show sel & #!4 atoms

> select up

2625 atoms, 2564 bonds, 103 pseudobonds, 195 residues, 23 models selected  

> show sel & #!4 atoms

> select clear

> select #4/B:202@O2

1 atom, 1 residue, 1 model selected  

> select ::display & solvent

Nothing selected  

> select @@display & solvent

83 atoms, 53 bonds, 30 residues, 6 models selected  

> select solvent

3517 atoms, 2150 bonds, 1367 residues, 7 models selected  

> select #4/B:202@O2

1 atom, 1 residue, 1 model selected  

> select add #4/B:203@O2

2 atoms, 2 residues, 1 model selected  

> select add #4/B:366@O

3 atoms, 3 residues, 1 model selected  

> select up

10 atoms, 7 bonds, 3 residues, 1 model selected  

> style sel ball

Changed 10 atom styles  

> select clear

> select add #4.1

11 pseudobonds, 1 model selected  

> ui tool show "Selection Inspector"

> setattr =sel p halfbond true

Assigning halfbond attribute to 11 items  

> setattr sel g halfbond true

Assigning halfbond attribute to 1 item  

> style sel dashes 0

Changed 1 pseudobond dash  

> setattr sel g radius 0.155

Assigning radius attribute to 1 item  

> select clear

> ui tool show "Crystal Contacts"

> crystalcontacts #4

11 pairs of asymmetric units of 8vhw contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
       298     0      9      1  1  0      0         1
        65     0      8      1  0  0      0         1
        64     0      8      1  1  0      0         1
        49     0      5      1  0  0      0         1
        37     0      4      0  1 -1      0         1
        32     0      0     -1  0  0      0         1
        30     0      0      1  0  0      0         1
        22     0      8      2  1  0      0         1
         9     0      4      0  0 -1      0         1
         6     0      5      0  0  0      0         1
         3     0      9      2  2  0      0         1
    

  

> hide #!7.1 models

> show #!7.1 models

> hide #!7 models

> show #!7 models

> hide #!7.2 models

> show #!7.2 models

> hide #!7.3 models

> hide #!7.4 models

> hide #!7.5 models

> hide #!7.6 models

> hide #!7.7 models

> hide #!7.8 models

> hide #!7.9 models

> hide #!7.10 models

> hide #!7.11 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.2 models

> combine #4 #7.1 name W161F

Remapping chain ID 'A' in 8vhw 1 1 0 sym 9 #7.1 to 'C'  
Remapping chain ID 'B' in 8vhw 1 1 0 sym 9 #7.1 to 'D'  

> hide #!7 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> close #4

> close #7

> select up

22 pseudobonds, 1 model selected  

> ui tool show "Selection Inspector"

> style sel dashes 0

Changed 1 pseudobond dash  

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #8/D:166

22 atoms, 22 bonds, 1 residue, 1 model selected  

> select add #8/D:162

37 atoms, 36 bonds, 2 residues, 1 model selected  

> show #!3 models

> hide #!3 models

> show sel atoms

> select clear

> select #8/c,d

7106 atoms, 6801 bonds, 11 pseudobonds, 793 residues, 2 models selected  

> color sel byhetero

> select clear

> mcopy #3 toAtoms #8 settings c

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!5 models

> mcopy #5 toAtoms #8 settings c

> show #!5 models

> show #!3 models

> hide #!5 models

> hide #!3 models

> mcopy #3 toAtoms #8 settings c

> select #8/B:201@MN

1 atom, 1 residue, 1 model selected  

> select sel @< 5

257 atoms, 197 bonds, 33 pseudobonds, 63 residues, 14 models selected  

> select up

897 atoms, 882 bonds, 33 pseudobonds, 63 residues, 14 models selected  

> select add #8/B:366@O

898 atoms, 882 bonds, 33 pseudobonds, 64 residues, 14 models selected  

> select add #8/D:166@DE2

899 atoms, 882 bonds, 33 pseudobonds, 65 residues, 14 models selected  

> select add #8/D:162@OE2

900 atoms, 882 bonds, 33 pseudobonds, 66 residues, 14 models selected  

> select up

937 atoms, 920 bonds, 33 pseudobonds, 66 residues, 14 models selected  

> select add #8/B:66

957 atoms, 940 bonds, 33 pseudobonds, 67 residues, 14 models selected  

> ui tool show H-Bonds

> select sel & !backbone

Expected a keyword  

> select sel & ~backbone

636 atoms, 614 bonds, 38 pseudobonds, 67 residues, 17 models selected  

> ui tool show H-Bonds

> hbonds sel color #00fdff dashes 6 interModel false twoColors true intraRes
> false select true reveal true retainCurrent true

W161F #8/A TYR 45 OH has bad number of bonds (3)  

W161F #8/A TYR 193 OH has bad number of bonds (3)  

W161F #8/C TYR 45 OH has bad number of bonds (3)  

W161F #8/C TYR 193 OH has bad number of bonds (3)  

42 hydrogen bonds found  

W161F #8/A TYR 45 OH has bad number of bonds (3)  

W161F #8/A TYR 193 OH has bad number of bonds (3)  

W161F #8/C TYR 45 OH has bad number of bonds (3)  

W161F #8/C TYR 193 OH has bad number of bonds (3)  

23 strict hydrogen bonds found  

> select clear

> delete pbonds sel

> select add #8.2

6 pseudobonds, 1 model selected  

> ui tool show "Selection Inspector"

> setattr =sel p halfbond true

Assigning halfbond attribute to 6 items  

> select clear

[Repeated 1 time(s)]

> undo

[Repeated 1 time(s)]

> 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  

> setattr sel g halfbond true

Assigning halfbond attribute to 1 item  

> setattr sel g halfbond false

Assigning halfbond attribute to 1 item  

> setattr sel g color #59eca9

Assigning color attribute to 1 item  

> setattr sel g color deepskyblue

Assigning color attribute to 1 item  

> setattr sel g color #00c0ff

Assigning color attribute to 1 item  

> setattr sel g color #00c1ff

Assigning color attribute to 1 item  

> setattr sel g color #00c6ff

Assigning color attribute to 1 item  

> setattr sel g color #00d6ff

Assigning color attribute to 1 item  

> setattr sel g color #00d7ff

Assigning color attribute to 1 item  

> setattr sel g color #00d8ff

Assigning color attribute to 1 item  

> setattr sel g color #00d9ff

Assigning color attribute to 1 item  

> setattr sel g color #00dbff

Assigning color attribute to 1 item  

> setattr sel g color #00ddff

Assigning color attribute to 1 item  

> setattr sel g color #00ebff

Assigning color attribute to 1 item  

> setattr sel g color #00f0ff

Assigning color attribute to 1 item  

> setattr sel g color #00f3ff

Assigning color attribute to 1 item  

> setattr sel g color #00f7ff

Assigning color attribute to 1 item  

> setattr sel g color #00f8ff

Assigning color attribute to 1 item  

> setattr sel g color #00f9ff

Assigning color attribute to 1 item  

> setattr sel g color #00f8ff

Assigning color attribute to 1 item  

> setattr sel g color #00f7ff

Assigning color attribute to 1 item  

> setattr sel g color #00f6ff

Assigning color attribute to 1 item  

> setattr sel g color #00f5ff

Assigning color attribute to 1 item  

> setattr sel g color #00f2ff

Assigning color attribute to 1 item  

> setattr sel g color #00f0ff

Assigning color attribute to 1 item  

> setattr sel g color #00efff

Assigning color attribute to 1 item  

> setattr sel g color #00edff

Assigning color attribute to 1 item  

> setattr sel g color #00ebff

Assigning color attribute to 1 item  

> setattr sel g color #00e9ff

Assigning color attribute to 1 item  

> setattr sel g color #00e8ff

Assigning color attribute to 1 item  

> setattr sel g color #00e5ff

Assigning color attribute to 1 item  

> setattr sel g color #00e2ff

Assigning color attribute to 1 item  

> setattr sel g color #00e0ff

Assigning color attribute to 1 item  

> setattr sel g color #00dfff

Assigning color attribute to 1 item  

> setattr sel g color #00deff

Assigning color attribute to 1 item  

> setattr sel g color #00ddff

Assigning color attribute to 1 item  

> setattr sel g color #0bddff

Assigning color attribute to 1 item  

> setattr sel g color #0cddff

Assigning color attribute to 1 item  

> setattr sel g color #0eddff

Assigning color attribute to 1 item  

> setattr sel g color #23ddff

Assigning color attribute to 1 item  

> setattr sel g color #35ddff

Assigning color attribute to 1 item  

> setattr sel g color #3addff

Assigning color attribute to 1 item  

> setattr sel g color #3cddff

Assigning color attribute to 1 item  

> setattr sel g color #3dddff

Assigning color attribute to 1 item  

> setattr sel g color #3cddff

Assigning color attribute to 1 item  

> setattr sel g color #3dddff

Assigning color attribute to 1 item  

> setattr sel g color #3fddff

Assigning color attribute to 1 item  

> setattr sel g color #45ddff

Assigning color attribute to 1 item  

> setattr sel g color #52ddff

Assigning color attribute to 1 item  

> setattr sel g color #56ddff

Assigning color attribute to 1 item  

> setattr sel g color #5cddff

Assigning color attribute to 1 item  

> setattr sel g color #5fddff

Assigning color attribute to 1 item  

> setattr sel g color #61ddff

Assigning color attribute to 1 item  

> setattr sel g color #63ddff

Assigning color attribute to 1 item  

> setattr sel g color #64ddff

Assigning color attribute to 1 item  

> setattr sel g color #65ddff

Assigning color attribute to 1 item  

> setattr sel g color #67ddff

Assigning color attribute to 1 item  

> setattr sel g color #66ddff

Assigning color attribute to 1 item  

> setattr sel g color #64ddff

Assigning color attribute to 1 item  

> setattr sel g color #63ddff

Assigning color attribute to 1 item  

> setattr sel g color #62ddff

Assigning color attribute to 1 item  

> setattr sel g color #61ddff

Assigning color attribute to 1 item  

> setattr sel g color #60ddff

Assigning color attribute to 1 item  

> setattr sel g color #5fddff

Assigning color attribute to 1 item  

> setattr sel g color #5eddff

Assigning color attribute to 1 item  

> setattr sel g color #5dddff

Assigning color attribute to 1 item  

> setattr sel g color #5bddff

Assigning color attribute to 1 item  

> setattr sel g color #58ddff

Assigning color attribute to 1 item  

> setattr sel g color #56ddff

Assigning color attribute to 1 item  

> setattr sel g color #55ddff

Assigning color attribute to 1 item  

> setattr sel g color #54ddff

Assigning color attribute to 1 item  

> setattr sel g color #53ddff

Assigning color attribute to 1 item  

> setattr sel g color #4fddff

Assigning color attribute to 1 item  

> setattr sel g color #2fddff

Assigning color attribute to 1 item  

> setattr sel g color #24ddff

Assigning color attribute to 1 item  

> setattr sel g color #11ddff

Assigning color attribute to 1 item  

> setattr sel g color #08ddff

Assigning color attribute to 1 item  

> setattr sel g color #00ddff

Assigning color attribute to 1 item  

> setattr sel g color #01ddff

Assigning color attribute to 1 item  

> setattr sel g color #08ddff

Assigning color attribute to 1 item  

> setattr sel g color #28ddff

Assigning color attribute to 1 item  

> setattr sel g color #29ddff

Assigning color attribute to 1 item  

> setattr sel g color #2addff

Assigning color attribute to 1 item  

> setattr sel g color #2bddff

Assigning color attribute to 1 item  

> setattr sel g color #2cddff

Assigning color attribute to 1 item  

> setattr sel g color #30ddff

Assigning color attribute to 1 item  

> setattr sel g color #37ddff

Assigning color attribute to 1 item  

> setattr sel g color #4dddff

Assigning color attribute to 1 item  

> setattr sel g color #55ddff

Assigning color attribute to 1 item  

> setattr sel g color #60ddff

Assigning color attribute to 1 item  

> setattr sel g color #61ddff

Assigning color attribute to 1 item  

> setattr sel g color #62ddff

Assigning color attribute to 1 item  

> setattr sel g color #64ddff

Assigning color attribute to 1 item  

> setattr sel g color #65ddff

Assigning color attribute to 1 item  

> setattr sel g color #67ddff

Assigning color attribute to 1 item  

> setattr sel g color #6addff

Assigning color attribute to 1 item  

> setattr sel g color #81ddff

Assigning color attribute to 1 item  

> setattr sel g color #85ddff

Assigning color attribute to 1 item  

> setattr sel g color #93ddff

Assigning color attribute to 1 item  

> setattr sel g color #95ddff

Assigning color attribute to 1 item  

> setattr sel g color #96ddff

Assigning color attribute to 1 item  

> setattr sel g color #98ddff

Assigning color attribute to 1 item  

> setattr sel g color #99ddff

Assigning color attribute to 1 item  

> setattr sel g color #9addff

Assigning color attribute to 1 item  

> setattr sel g color #9bddff

Assigning color attribute to 1 item  

> setattr sel g color #9cddff

Assigning color attribute to 1 item  

> setattr sel g color #a5ddff

Assigning color attribute to 1 item  

> setattr sel g color #aaddff

Assigning color attribute to 1 item  

> setattr sel g color #afddff

Assigning color attribute to 1 item  

> setattr sel g color #b0ddff

Assigning color attribute to 1 item  

> setattr sel g color #adddff

Assigning color attribute to 1 item  

> setattr sel g color #acddff

Assigning color attribute to 1 item  

> setattr sel g color #a6ddff

Assigning color attribute to 1 item  

> setattr sel g color #9fddff

Assigning color attribute to 1 item  

> setattr sel g color #9bddff

Assigning color attribute to 1 item  

> setattr sel g color #94ddff

Assigning color attribute to 1 item  

> setattr sel g color #8eddff

Assigning color attribute to 1 item  

> setattr sel g color #8bddff

Assigning color attribute to 1 item  

> setattr sel g color #81ddff

Assigning color attribute to 1 item  

> setattr sel g color #7eddff

Assigning color attribute to 1 item  

> setattr sel g color #7dddff

Assigning color attribute to 1 item  

> setattr sel g color #7cddff

Assigning color attribute to 1 item  

> setattr sel g color #7bddff

Assigning color attribute to 1 item  

> setattr sel g color #7addff

Assigning color attribute to 1 item  

> setattr sel g color #7bddff

Assigning color attribute to 1 item  

> setattr sel g color #7dddff

Assigning color attribute to 1 item  

> setattr sel g color #7eddff

Assigning color attribute to 1 item  

> setattr sel g color #80ddff

Assigning color attribute to 1 item  

> setattr sel g color #7fddff

Assigning color attribute to 1 item  

> setattr sel g color #7eddff

Assigning color attribute to 1 item  

> setattr sel g color #7cddff

Assigning color attribute to 1 item  

> setattr sel g color #79ddff

Assigning color attribute to 1 item  

> setattr sel g color #72ddff

Assigning color attribute to 1 item  

> setattr sel g color #6cddff

Assigning color attribute to 1 item  

> setattr sel g color #5cddff

Assigning color attribute to 1 item  

> setattr sel g color #56ddff

Assigning color attribute to 1 item  

> setattr sel g color #31ddff

Assigning color attribute to 1 item  

> setattr sel g color #29ddff

Assigning color attribute to 1 item  

> setattr sel g color #18ddff

Assigning color attribute to 1 item  

> setattr sel g color #0fddff

Assigning color attribute to 1 item  

> setattr sel g color #07ddff

Assigning color attribute to 1 item  

> setattr sel g color #00ddff

Assigning color attribute to 1 item  

> select add #8.2

6 pseudobonds, 1 model selected  

> color #8.2 #00fdffff models

> color #8.2 #aa7942ff models

> color #8.2 #00fdffff models

> select clear

> show #!3 models

> hide #8.2 models

> show #8.2 models

> show #!6 models

> hide #!6 models

> close #6

> hide #!8 models

> hide #!3 models

> show #!3 models

> ui tool show "Selection Inspector"

> hide #!3 models

> show #!8 models

> ui tool show "Selection Inspector"

> style sel dashes 10

Changed 1 pseudobond dash  

> style sel dashes 6

Changed 1 pseudobond dash  

> select #8/B:203@DO1

1 atom, 1 residue, 1 model selected  

> select add #8/B:34@OH

2 atoms, 2 residues, 1 model selected  

> select add #8/B:203@O1

3 atoms, 2 residues, 1 model selected  

> select add #8/B:30@DD1

4 atoms, 3 residues, 1 model selected  

> style sel dashes 10

Changed 1 pseudobond dash  

> style sel dashes 6

Changed 1 pseudobond dash  

> select clear

> delete pbonds sel

> select #8/B:30@DD1

1 atom, 1 residue, 1 model selected  

> select add #8/B:203@O1

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select #8/B:203@DO1

1 atom, 1 residue, 1 model selected  

> select add #8/B:34@OH

2 atoms, 2 residues, 1 model selected  

> pbond sel

> select #8/B:143@DE22

1 atom, 1 residue, 1 model selected  

> select add #8/B:202@O2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> ui tool show "Selection Inspector"

> setattr sel g halfbond true

Assigning halfbond attribute to 1 item  

> style sel dashes 10

Changed 1 pseudobond dash  

> select clear

> delete pbonds sel

> select #8/D:166@DH

1 atom, 1 residue, 1 model selected  

> select add #8/B:30@NE2

2 atoms, 2 residues, 1 model selected  

> pbond sel

> ui tool show "Selection Inspector"

[Repeated 1 time(s)]

> 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  

> select clear

> select #8/B:366@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/W161F-MnSOD-
> Peroxide2.png" width 1244 height 859 supersample 4

> view name W161F-PEO2

> select #8/B:161@DD1

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 20 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/W161F-MnSOD-
> Peroxide1.png" width 1244 height 859 supersample 4

> view name W161F-PEO1

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/W161F-MnSOD-
> Peroxide1.tif" width 1244 height 859 supersample 4

> view name W161F-PEO1

[Repeated 1 time(s)]

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/W161F-MnSOD-
> Peroxide1.tif" width 1244 height 859 supersample 4

> view W161F-PEO2

> view name W161F-PEO2

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/W161F-MnSOD-
> Peroxide2.tif" width 1244 height 859 supersample 4

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl
> Lab/Papers/Manuscripts/Medhanjali MnSOD mini review/MnSOD_W161F.cxs"

——— End of log from Tue Aug 19 16:03:40 2025 ———

> view name session-start

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 74, in pbg_update  
self._update_graphics()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 213, in _update_graphics  
elif self.num_pseudobonds == 0:  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "changes":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 74, in pbg_update  
self._update_graphics()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 213, in _update_graphics  
elif self.num_pseudobonds == 0:  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "changes":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 74, in pbg_update  
self._update_graphics()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 213, in _update_graphics  
elif self.num_pseudobonds == 0:  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "changes":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 196, in _update_graphics_if_needed  
gc = self._graphics_changed  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "graphics update":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 196, in _update_graphics_if_needed  
gc = self._graphics_changed  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "graphics update":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 196, in _update_graphics_if_needed  
gc = self._graphics_changed  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "graphics update":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 218, in <lambda>  
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 247, in _fill_tree  
all_selected_models = self.session.selection.models(all_selected=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/selection.py", line 40, in models  
return [m for m in self._all_models if m.get_selected(include_children=True,
fully=True)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/selection.py", line 40, in <listcomp>  
return [m for m in self._all_models if m.get_selected(include_children=True,
fully=True)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 108, in get_selected  
if self.pseudobonds.num_selected < self.num_pseudobonds:  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 179, in get_prop  
vcount = getattr(self, value_count)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
Error processing trigger "new frame":  
AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 111, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,7
      Model Number: Z1FU000A9LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 16 days, 17 hours, 23 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

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