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UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open "C:/Users/moham/Downloads/Chimera Testing Grounds/wFAP0.pdb"

Summary of feedback from opening C:/Users/moham/Downloads/Chimera Testing Grounds/wFAP0.pdb
warning	Ignored bad PDB record found on line 3019

Chain information for wFAP0.pdb #1
Chain	Description
A	No description available

Computing secondary structure

open "C:\Users\moham\Downloads\Chimera Testing Grounds\wFAP0.pdb" format pdb

Summary of feedback from opening C:\Users\moham\Downloads\Chimera Testing Grounds\wFAP0.pdb
warning	Ignored bad PDB record found on line 3019

Chain information for wFAP0.pdb #2
Chain	Description
A	No description available

Computing secondary structure

open https://rbvi.ucsf.edu/chimerax/docs/user/formats/kdHydrophobicity.defattr

Summary of feedback from opening //rbvi.ucsf.edu/chimerax/docs/user/formats/kdHydrophobicity.defattr fetched from https
notes	Fetching compressed kdHydrophobicity(1).defattr from https://rbvi.ucsf.edu/chimerax/docs/user/formats/kdHydrophobicity.defattr Downloaded kdHydrophobicity.defattr to C:\Users\moham\Downloads\kdHydrophobicity(1).defattr Assigned attribute 'kdHydrophobicity' to 322 residues using match mode: any

select /b

86 atoms, 90 bonds, 2 residues, 2 models selected

select up

5942 atoms, 5962 bonds, 324 residues, 2 models selected

select up

5942 atoms, 5962 bonds, 324 residues, 2 models selected

select down

86 atoms, 90 bonds, 2 residues, 2 models selected

select /B :< 5 & ~/B

1114 atoms, 1072 bonds, 66 residues, 2 models selected

color byattribute residue.kdHydrophobicity palette yellow:white:blue target a

No known/registered numeric attribute residue.kdHydrophobicity

color sel byattribute residue.kdHydrophobicity palette yellow:white:blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword

color byattribute r:kdHydrophobicity target sabc palette -4.5,blue:0,white:4.5,red

5942 atoms, 324 residues, atom kdHydrophobicity range -4.5 to 4.5

color byattribute r:kdHydrophobicity target sabc palette -4.5,blue:0,white:4.5,red

5942 atoms, 324 residues, atom kdHydrophobicity range -4.5 to 4.5

undo

[Repeated 1 time(s)]

color sel byattribute r:kdHydrophobicity target sabc palette -4.5,blue:0,white:4.5,red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword

color byattribute residue.kdHydrophobicity palette yellow:white:blue

No known/registered numeric attribute residue.kdHydrophobicity

color byattribute r:kdHydrophobicity target sabc palette -4.5,blue:0,white:4.5,red

5942 atoms, 324 residues, atom kdHydrophobicity range -4.5 to 4.5

select /a & ~sel

4742 atoms, 4704 bonds, 256 residues, 2 models selected

color sel beige

color sel peachpuff

color sel lime

select /A

5856 atoms, 5872 bonds, 322 residues, 2 models selected

show sel surfaces

transparency #1.1 30

hide #!2 models

show #!2 models

hide #!2 models

show #!2 models

transparency #1.1 30

close #2

transparency #1.1 70

select /B

43 atoms, 45 bonds, 1 residue, 1 model selected

select sel @< 5

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

select /A & ~sel

2662 atoms, 2631 bonds, 159 residues, 1 model selected

color (#!1 & sel) cyan

ui tool show "Color Actions"

undo

color sel cyan target acpf

undo

"Unable to open monitor interface to \\\\.\\DISPLAY1:" "Unknown error 0xe0000225."

[Repeated 29 time(s)]

select /B

43 atoms, 45 bonds, 1 residue, 1 model selected

select /B :< 5 & ~/B

557 atoms, 536 bonds, 33 residues, 1 model selected

label (#!1 & sel) attribute name

ui tool show "Color Actions"

[Repeated 1 time(s)]

color sel black target acpf

[Repeated 1 time(s)]

undo

[Repeated 1 time(s)]

select /A & ~sel

2371 atoms, 2352 bonds, 128 residues, 1 model selected

color sel yellow target acpf

select /A & ~sel

557 atoms, 536 bonds, 33 residues, 1 model selected

label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png

save "C:/Users/moham/Downloads/Chimera Testing Grounds"

Cannot determine format for 'C:/Users/moham/Downloads/Chimera Testing Grounds'

save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png

save "C:/Users/moham/Downloads/Chimera Testing Grounds/#2.png"

select ~sel & ##selected

2414 atoms, 2445 bonds, 129 residues, 1 model selected

select ~sel & ##selected

557 atoms, 536 bonds, 33 residues, 1 model selected

save "C:/Users/moham/Downloads/Chimera Testing Grounds/#2B.png"

save "C:/Users/moham/Downloads/Chimera Testing Grounds/#2C.png"

select /B

43 atoms, 45 bonds, 1 residue, 1 model selected

select /B :< 5 & ~/B

557 atoms, 536 bonds, 33 residues, 1 model selected

"Unable to open monitor interface to \\\\.\\DISPLAY1:" "Unknown error 0xe0000225."

[Repeated 13 time(s)]

color sel blue

select clear

undo

[Repeated 1 time(s)]

ui tool show "Color Actions"

color sel blue target acpf

hide #1.1 models

select clear

hide #1.2 models

name frozen 5A sel

Not registering illegal selector name "5A"

name frozen A sel

select A

2928 atoms, 536 bonds, 161 residues, 1 model selected

name frozen fiveA A

select A

2928 atoms, 536 bonds, 161 residues, 1 model selected

select fiveAA

Expected an objects specifier or a keyword

select fiveA

2928 atoms, 536 bonds, 161 residues, 1 model selected

name delete A

color fiveA byattribute residue.charge

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword

color fiveA byattribute charge

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword

coulombic

Using Amber 20 recommended default charges and atom types for standard residues
Coulombic values for wFAP0.pdb_A SES surface #1.1: minimum, -14.61, mean -1.11, maximum 10.52

hide #1.1 models

show #1.1 models

undo

color byattribute charge palette red:white:blue sel atoms

Expected a keyword

color byattribute charge palette red:white:blue sel

Expected a keyword

color byattribute charge palette red:white:blue atoms

Expected a keyword

color byattribute charge sel

2928 atoms, 161 residues, 1 surfaces, atom charge range -0.919 to 0.819

info atoms sel

atom id /A:1@N idatm_type N3+
atom id /A:1@CA idatm_type C3
atom id /A:1@C idatm_type C2
atom id /A:1@O idatm_type O2
atom id /A:1@CB idatm_type C3
atom id /A:1@CG idatm_type Cac
atom id /A:1@OD1 idatm_type O2-
atom id /A:1@OD2 idatm_type O2-
atom id /A:1@1H idatm_type H
atom id /A:1@2H idatm_type H
atom id /A:1@3H idatm_type H
atom id /A:1@HA idatm_type HC
atom id /A:1@1HB idatm_type HC
atom id /A:1@2HB idatm_type HC
atom id /A:2@N idatm_type Npl
atom id /A:2@CA idatm_type C3
atom id /A:2@C idatm_type C2
atom id /A:2@O idatm_type O2
atom id /A:2@CB idatm_type C3
atom id /A:2@CG idatm_type C3
atom id /A:2@CD idatm_type Cac
atom id /A:2@OE1 idatm_type O2-
atom id /A:2@OE2 idatm_type O2-
atom id /A:2@H idatm_type H
atom id /A:2@HA idatm_type HC
atom id /A:2@1HB idatm_type HC
atom id /A:2@2HB idatm_type HC
atom id /A:2@1HG idatm_type HC
atom id /A:2@2HG idatm_type HC
atom id /A:3@N idatm_type Npl
atom id /A:3@CA idatm_type C3
atom id /A:3@C idatm_type C2
atom id /A:3@O idatm_type O2
atom id /A:3@CB idatm_type C3
atom id /A:3@CG idatm_type C3
atom id /A:3@CD idatm_type Cac
atom id /A:3@OE1 idatm_type O2-
atom id /A:3@OE2 idatm_type O2-
atom id /A:3@H idatm_type H
atom id /A:3@HA idatm_type HC
atom id /A:3@1HB idatm_type HC
atom id /A:3@2HB idatm_type HC
atom id /A:3@1HG idatm_type HC
atom id /A:3@2HG idatm_type HC
atom id /A:4@N idatm_type Npl
atom id /A:4@CA idatm_type C3
atom id /A:4@C idatm_type C2
atom id /A:4@O idatm_type O2
atom id /A:4@CB idatm_type C3
atom id /A:4@CG idatm_type C3
atom id /A:4@CD idatm_type C3
atom id /A:4@NE idatm_type Ng+
atom id /A:4@CZ idatm_type C2
atom id /A:4@NH1 idatm_type Ng+
atom id /A:4@NH2 idatm_type Ng+
atom id /A:4@H idatm_type H
atom id /A:4@HA idatm_type HC
atom id /A:4@1HB idatm_type HC
atom id /A:4@2HB idatm_type HC
atom id /A:4@1HG idatm_type HC
atom id /A:4@2HG idatm_type HC
atom id /A:4@1HD idatm_type HC
atom id /A:4@2HD idatm_type HC
atom id /A:4@HE idatm_type H
atom id /A:4@1HH1 idatm_type H
atom id /A:4@2HH1 idatm_type H
atom id /A:4@1HH2 idatm_type H
atom id /A:4@2HH2 idatm_type H
atom id /A:5@N idatm_type Npl
atom id /A:5@CA idatm_type C3
atom id /A:5@C idatm_type C2
atom id /A:5@O idatm_type O2
atom id /A:5@CB idatm_type C3
atom id /A:5@CG idatm_type C3
atom id /A:5@CD1 idatm_type C3
atom id /A:5@CD2 idatm_type C3
atom id /A:5@H idatm_type H
atom id /A:5@HA idatm_type HC
atom id /A:5@1HB idatm_type HC
atom id /A:5@2HB idatm_type HC
atom id /A:5@HG idatm_type HC
atom id /A:5@1HD1 idatm_type HC
atom id /A:5@2HD1 idatm_type HC
atom id /A:5@3HD1 idatm_type HC
atom id /A:5@1HD2 idatm_type HC
atom id /A:5@2HD2 idatm_type HC
atom id /A:5@3HD2 idatm_type HC
atom id /A:6@N idatm_type Npl
atom id /A:6@CA idatm_type C3
atom id /A:6@C idatm_type C2
atom id /A:6@O idatm_type O2
atom id /A:6@CB idatm_type C3
atom id /A:6@CG idatm_type C3
atom id /A:6@CD idatm_type C3
atom id /A:6@CE idatm_type C3
atom id /A:6@NZ idatm_type N3+
atom id /A:6@H idatm_type H
atom id /A:6@HA idatm_type HC
atom id /A:6@1HB idatm_type HC
atom id /A:6@2HB idatm_type HC
atom id /A:6@1HG idatm_type HC
atom id /A:6@2HG idatm_type HC
atom id /A:6@1HD idatm_type HC
atom id /A:6@2HD idatm_type HC
atom id /A:6@1HE idatm_type HC
atom id /A:6@2HE idatm_type HC
atom id /A:6@1HZ idatm_type H
atom id /A:6@2HZ idatm_type H
atom id /A:6@3HZ idatm_type H
atom id /A:7@N idatm_type Npl
atom id /A:7@CA idatm_type C3
atom id /A:7@C idatm_type C2
atom id /A:7@O idatm_type O2
atom id /A:7@CB idatm_type C3
atom id /A:7@CG idatm_type C3
atom id /A:7@CD idatm_type Cac
atom id /A:7@OE1 idatm_type O2-
atom id /A:7@OE2 idatm_type O2-
atom id /A:7@H idatm_type H
atom id /A:7@HA idatm_type HC
atom id /A:7@1HB idatm_type HC
atom id /A:7@2HB idatm_type HC
atom id /A:7@1HG idatm_type HC
atom id /A:7@2HG idatm_type HC
atom id /A:8@N idatm_type Npl
atom id /A:8@CA idatm_type C3
atom id /A:8@C idatm_type C2
atom id /A:8@O idatm_type O2
atom id /A:8@CB idatm_type C3
atom id /A:8@CG1 idatm_type C3
atom id /A:8@CG2 idatm_type C3
atom id /A:8@CD1 idatm_type C3
atom id /A:8@H idatm_type H
atom id /A:8@HA idatm_type HC
atom id /A:8@HB idatm_type HC
atom id /A:8@1HG1 idatm_type HC
atom id /A:8@2HG1 idatm_type HC
atom id /A:8@1HG2 idatm_type HC
atom id /A:8@2HG2 idatm_type HC
atom id /A:8@3HG2 idatm_type HC
atom id /A:8@1HD1 idatm_type HC
atom id /A:8@2HD1 idatm_type HC
atom id /A:8@3HD1 idatm_type HC
atom id /A:9@N idatm_type Npl
atom id /A:9@CA idatm_type C3
atom id /A:9@C idatm_type C2
atom id /A:9@O idatm_type O2
atom id /A:9@CB idatm_type C3
atom id /A:9@CG idatm_type C3
atom id /A:9@CD1 idatm_type C3
atom id /A:9@CD2 idatm_type C3
atom id /A:9@H idatm_type H
atom id /A:9@HA idatm_type HC
atom id /A:9@1HB idatm_type HC
atom id /A:9@2HB idatm_type HC
atom id /A:9@HG idatm_type HC
atom id /A:9@1HD1 idatm_type HC
atom id /A:9@2HD1 idatm_type HC
atom id /A:9@3HD1 idatm_type HC
atom id /A:9@1HD2 idatm_type HC
atom id /A:9@2HD2 idatm_type HC
atom id /A:9@3HD2 idatm_type HC
atom id /A:10@N idatm_type Npl
atom id /A:10@CA idatm_type C3
atom id /A:10@C idatm_type C2
atom id /A:10@O idatm_type O2
atom id /A:10@CB idatm_type C3
atom id /A:10@CG idatm_type C3
atom id /A:10@CD idatm_type Cac
atom id /A:10@OE1 idatm_type O2-
atom id /A:10@OE2 idatm_type O2-
atom id /A:10@H idatm_type H
atom id /A:10@HA idatm_type HC
atom id /A:10@1HB idatm_type HC
atom id /A:10@2HB idatm_type HC
atom id /A:10@1HG idatm_type HC
atom id /A:10@2HG idatm_type HC
atom id /A:11@N idatm_type Npl
atom id /A:11@CA idatm_type C3
atom id /A:11@C idatm_type C2
atom id /A:11@O idatm_type O2
atom id /A:11@CB idatm_type C3
atom id /A:11@CG idatm_type C3
atom id /A:11@CD idatm_type Cac
atom id /A:11@OE1 idatm_type O2-
atom id /A:11@OE2 idatm_type O2-
atom id /A:11@H idatm_type H
atom id /A:11@HA idatm_type HC
atom id /A:11@1HB idatm_type HC
atom id /A:11@2HB idatm_type HC
atom id /A:11@1HG idatm_type HC
atom id /A:11@2HG idatm_type HC
atom id /A:12@N idatm_type Npl
atom id /A:12@CA idatm_type C3
atom id /A:12@C idatm_type C2
atom id /A:12@O idatm_type O2
atom id /A:12@CB idatm_type C3
atom id /A:12@CG idatm_type C3
atom id /A:12@CD1 idatm_type C3
atom id /A:12@CD2 idatm_type C3
atom id /A:12@H idatm_type H
atom id /A:12@HA idatm_type HC
atom id /A:12@1HB idatm_type HC
atom id /A:12@2HB idatm_type HC
atom id /A:12@HG idatm_type HC
atom id /A:12@1HD1 idatm_type HC
atom id /A:12@2HD1 idatm_type HC
atom id /A:12@3HD1 idatm_type HC
atom id /A:12@1HD2 idatm_type HC
atom id /A:12@2HD2 idatm_type HC
atom id /A:12@3HD2 idatm_type HC
atom id /A:13@N idatm_type Npl
atom id /A:13@CA idatm_type C3
atom id /A:13@C idatm_type C2
atom id /A:13@O idatm_type O2
atom id /A:13@CB idatm_type C3
atom id /A:13@CG idatm_type C3
atom id /A:13@CD idatm_type Cac
atom id /A:13@OE1 idatm_type O2-
atom id /A:13@OE2 idatm_type O2-
atom id /A:13@H idatm_type H
atom id /A:13@HA idatm_type HC
atom id /A:13@1HB idatm_type HC
atom id /A:13@2HB idatm_type HC
atom id /A:13@1HG idatm_type HC
atom id /A:13@2HG idatm_type HC
atom id /A:14@N idatm_type Npl
atom id /A:14@CA idatm_type C3
atom id /A:14@C idatm_type C2
atom id /A:14@O idatm_type O2
atom id /A:14@CB idatm_type C3
atom id /A:14@CG idatm_type C3
atom id /A:14@CD idatm_type C3
atom id /A:14@NE idatm_type Ng+
atom id /A:14@CZ idatm_type C2
atom id /A:14@NH1 idatm_type Ng+
atom id /A:14@NH2 idatm_type Ng+
atom id /A:14@H idatm_type H
atom id /A:14@HA idatm_type HC
atom id /A:14@1HB idatm_type HC
atom id /A:14@2HB idatm_type HC
atom id /A:14@1HG idatm_type HC
atom id /A:14@2HG idatm_type HC
atom id /A:14@1HD idatm_type HC
atom id /A:14@2HD idatm_type HC
atom id /A:14@HE idatm_type H
atom id /A:14@1HH1 idatm_type H
atom id /A:14@2HH1 idatm_type H
atom id /A:14@1HH2 idatm_type H
atom id /A:14@2HH2 idatm_type H
atom id /A:15@N idatm_type Npl
atom id /A:15@CA idatm_type C3
atom id /A:15@C idatm_type C2
atom id /A:15@O idatm_type O2
atom id /A:15@CB idatm_type C3
atom id /A:15@CG1 idatm_type C3
atom id /A:15@CG2 idatm_type C3
atom id /A:15@CD1 idatm_type C3
atom id /A:15@H idatm_type H
atom id /A:15@HA idatm_type HC
atom id /A:15@HB idatm_type HC
atom id /A:15@1HG1 idatm_type HC
atom id /A:15@2HG1 idatm_type HC
atom id /A:15@1HG2 idatm_type HC
atom id /A:15@2HG2 idatm_type HC
atom id /A:15@3HG2 idatm_type HC
atom id /A:15@1HD1 idatm_type HC
atom id /A:15@2HD1 idatm_type HC
atom id /A:15@3HD1 idatm_type HC
atom id /A:16@N idatm_type Npl
atom id /A:16@CA idatm_type C3
atom id /A:16@C idatm_type C2
atom id /A:16@O idatm_type O2
atom id /A:16@CB idatm_type C3
atom id /A:16@CG1 idatm_type C3
atom id /A:16@CG2 idatm_type C3
atom id /A:16@CD1 idatm_type C3
atom id /A:16@H idatm_type H
atom id /A:16@HA idatm_type HC
atom id /A:16@HB idatm_type HC
atom id /A:16@1HG1 idatm_type HC
atom id /A:16@2HG1 idatm_type HC
atom id /A:16@1HG2 idatm_type HC
atom id /A:16@2HG2 idatm_type HC
atom id /A:16@3HG2 idatm_type HC
atom id /A:16@1HD1 idatm_type HC
atom id /A:16@2HD1 idatm_type HC
atom id /A:16@3HD1 idatm_type HC
atom id /A:17@N idatm_type Npl
atom id /A:17@CA idatm_type C3
atom id /A:17@C idatm_type C2
atom id /A:17@O idatm_type O2
atom id /A:17@CB idatm_type C3
atom id /A:17@CG idatm_type C3
atom id /A:17@CD idatm_type Cac
atom id /A:17@OE1 idatm_type O2-
atom id /A:17@OE2 idatm_type O2-
atom id /A:17@H idatm_type H
atom id /A:17@HA idatm_type HC
atom id /A:17@1HB idatm_type HC
atom id /A:17@2HB idatm_type HC
atom id /A:17@1HG idatm_type HC
atom id /A:17@2HG idatm_type HC
atom id /A:18@N idatm_type Npl
atom id /A:18@CA idatm_type C3
atom id /A:18@C idatm_type C2
atom id /A:18@O idatm_type O2
atom id /A:18@CB idatm_type C3
atom id /A:18@CG idatm_type C3
atom id /A:18@CD idatm_type Cac
atom id /A:18@OE1 idatm_type O2-
atom id /A:18@OE2 idatm_type O2-
atom id /A:18@H idatm_type H
atom id /A:18@HA idatm_type HC
atom id /A:18@1HB idatm_type HC
atom id /A:18@2HB idatm_type HC
atom id /A:18@1HG idatm_type HC
atom id /A:18@2HG idatm_type HC
atom id /A:19@N idatm_type Npl
atom id /A:19@CA idatm_type C3
atom id /A:19@C idatm_type C2
atom id /A:19@O idatm_type O2
atom id /A:19@CB idatm_type C3
atom id /A:19@CG1 idatm_type C3
atom id /A:19@CG2 idatm_type C3
atom id /A:19@H idatm_type H
atom id /A:19@HA idatm_type HC
atom id /A:19@HB idatm_type HC
atom id /A:19@1HG1 idatm_type HC
atom id /A:19@2HG1 idatm_type HC
atom id /A:19@3HG1 idatm_type HC
atom id /A:19@1HG2 idatm_type HC
atom id /A:19@2HG2 idatm_type HC
atom id /A:19@3HG2 idatm_type HC
atom id /A:20@N idatm_type Npl
atom id /A:20@CA idatm_type C3
atom id /A:20@C idatm_type C2
atom id /A:20@O idatm_type O2
atom id /A:20@CB idatm_type C3
atom id /A:20@CG idatm_type C3
atom id /A:20@CD idatm_type C3
atom id /A:20@CE idatm_type C3
atom id /A:20@NZ idatm_type N3+
atom id /A:20@H idatm_type H
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atom id /A:21@NH2 idatm_type Ng+
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atom id /A:22@N idatm_type Npl
atom id /A:22@CA idatm_type C3
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atom id /A:23@N idatm_type Npl
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atom id /A:24@N idatm_type Npl
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atom id /A:25@N idatm_type Npl
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atom id /A:25@CB idatm_type C3
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atom id /A:25@NZ idatm_type N3+
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atom id /A:26@N idatm_type Npl
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atom id /A:27@CA idatm_type C3
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atom id /A:27@H idatm_type H
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atom id /A:28@N idatm_type Npl
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atom id /A:28@NH1 idatm_type Ng+
atom id /A:28@NH2 idatm_type Ng+
atom id /A:28@H idatm_type H
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atom id /A:29@N idatm_type Npl
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atom id /A:30@N idatm_type Npl
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atom id /A:30@3HD2 idatm_type HC
atom id /A:31@N idatm_type Npl
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atom id /A:31@NH2 idatm_type Ng+
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atom id /A:34@CE2 idatm_type Car
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atom id /A:44@CE2 idatm_type Car
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atom id /A:45@NH2 idatm_type Ng+
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atom id /A:150@2HB idatm_type HC
atom id /A:150@1HG idatm_type HC
atom id /A:150@2HG idatm_type HC
atom id /A:151@N idatm_type Npl
atom id /A:151@CA idatm_type C3
atom id /A:151@C idatm_type C2
atom id /A:151@O idatm_type O2
atom id /A:151@CB idatm_type C3
atom id /A:151@CG idatm_type C3
atom id /A:151@CD idatm_type C3
atom id /A:151@NE idatm_type Ng+
atom id /A:151@CZ idatm_type C2
atom id /A:151@NH1 idatm_type Ng+
atom id /A:151@NH2 idatm_type Ng+
atom id /A:151@H idatm_type H
atom id /A:151@HA idatm_type HC
atom id /A:151@1HB idatm_type HC
atom id /A:151@2HB idatm_type HC
atom id /A:151@1HG idatm_type HC
atom id /A:151@2HG idatm_type HC
atom id /A:151@1HD idatm_type HC
atom id /A:151@2HD idatm_type HC
atom id /A:151@HE idatm_type H
atom id /A:151@1HH1 idatm_type H
atom id /A:151@2HH1 idatm_type H
atom id /A:151@1HH2 idatm_type H
atom id /A:151@2HH2 idatm_type H
atom id /A:152@N idatm_type Npl
atom id /A:152@CA idatm_type C3
atom id /A:152@C idatm_type C2
atom id /A:152@O idatm_type O2
atom id /A:152@CB idatm_type C3
atom id /A:152@CG idatm_type C3
atom id /A:152@CD1 idatm_type C3
atom id /A:152@CD2 idatm_type C3
atom id /A:152@H idatm_type H
atom id /A:152@HA idatm_type HC
atom id /A:152@1HB idatm_type HC
atom id /A:152@2HB idatm_type HC
atom id /A:152@HG idatm_type HC
atom id /A:152@1HD1 idatm_type HC
atom id /A:152@2HD1 idatm_type HC
atom id /A:152@3HD1 idatm_type HC
atom id /A:152@1HD2 idatm_type HC
atom id /A:152@2HD2 idatm_type HC
atom id /A:152@3HD2 idatm_type HC
atom id /A:153@N idatm_type Npl
atom id /A:153@CA idatm_type C3
atom id /A:153@C idatm_type C2
atom id /A:153@O idatm_type O2
atom id /A:153@CB idatm_type C3
atom id /A:153@CG idatm_type C3
atom id /A:153@CD1 idatm_type C3
atom id /A:153@CD2 idatm_type C3
atom id /A:153@H idatm_type H
atom id /A:153@HA idatm_type HC
atom id /A:153@1HB idatm_type HC
atom id /A:153@2HB idatm_type HC
atom id /A:153@HG idatm_type HC
atom id /A:153@1HD1 idatm_type HC
atom id /A:153@2HD1 idatm_type HC
atom id /A:153@3HD1 idatm_type HC
atom id /A:153@1HD2 idatm_type HC
atom id /A:153@2HD2 idatm_type HC
atom id /A:153@3HD2 idatm_type HC
atom id /A:154@N idatm_type Npl
atom id /A:154@CA idatm_type C3
atom id /A:154@C idatm_type C2
atom id /A:154@O idatm_type O2
atom id /A:154@CB idatm_type C3
atom id /A:154@CG idatm_type C3
atom id /A:154@CD idatm_type C3
atom id /A:154@NE idatm_type Ng+
atom id /A:154@CZ idatm_type C2
atom id /A:154@NH1 idatm_type Ng+
atom id /A:154@NH2 idatm_type Ng+
atom id /A:154@H idatm_type H
atom id /A:154@HA idatm_type HC
atom id /A:154@1HB idatm_type HC
atom id /A:154@2HB idatm_type HC
atom id /A:154@1HG idatm_type HC
atom id /A:154@2HG idatm_type HC
atom id /A:154@1HD idatm_type HC
atom id /A:154@2HD idatm_type HC
atom id /A:154@HE idatm_type H
atom id /A:154@1HH1 idatm_type H
atom id /A:154@2HH1 idatm_type H
atom id /A:154@1HH2 idatm_type H
atom id /A:154@2HH2 idatm_type H
atom id /A:155@N idatm_type Npl
atom id /A:155@CA idatm_type C3
atom id /A:155@C idatm_type C2
atom id /A:155@O idatm_type O2
atom id /A:155@CB idatm_type C3
atom id /A:155@CG idatm_type C3
atom id /A:155@CD idatm_type C3
atom id /A:155@NE idatm_type Ng+
atom id /A:155@CZ idatm_type C2
atom id /A:155@NH1 idatm_type Ng+
atom id /A:155@NH2 idatm_type Ng+
atom id /A:155@H idatm_type H
atom id /A:155@HA idatm_type HC
atom id /A:155@1HB idatm_type HC
atom id /A:155@2HB idatm_type HC
atom id /A:155@1HG idatm_type HC
atom id /A:155@2HG idatm_type HC
atom id /A:155@1HD idatm_type HC
atom id /A:155@2HD idatm_type HC
atom id /A:155@HE idatm_type H
atom id /A:155@1HH1 idatm_type H
atom id /A:155@2HH1 idatm_type H
atom id /A:155@1HH2 idatm_type H
atom id /A:155@2HH2 idatm_type H
atom id /A:156@N idatm_type Npl
atom id /A:156@CA idatm_type C3
atom id /A:156@C idatm_type C2
atom id /A:156@O idatm_type O2
atom id /A:156@CB idatm_type C3
atom id /A:156@CG idatm_type C3
atom id /A:156@CD1 idatm_type C3
atom id /A:156@CD2 idatm_type C3
atom id /A:156@H idatm_type H
atom id /A:156@HA idatm_type HC
atom id /A:156@1HB idatm_type HC
atom id /A:156@2HB idatm_type HC
atom id /A:156@HG idatm_type HC
atom id /A:156@1HD1 idatm_type HC
atom id /A:156@2HD1 idatm_type HC
atom id /A:156@3HD1 idatm_type HC
atom id /A:156@1HD2 idatm_type HC
atom id /A:156@2HD2 idatm_type HC
atom id /A:156@3HD2 idatm_type HC
atom id /A:157@N idatm_type Npl
atom id /A:157@CA idatm_type C3
atom id /A:157@C idatm_type C2
atom id /A:157@O idatm_type O2
atom id /A:157@CB idatm_type C3
atom id /A:157@CG idatm_type C3
atom id /A:157@CD1 idatm_type C3
atom id /A:157@CD2 idatm_type C3
atom id /A:157@H idatm_type H
atom id /A:157@HA idatm_type HC
atom id /A:157@1HB idatm_type HC
atom id /A:157@2HB idatm_type HC
atom id /A:157@HG idatm_type HC
atom id /A:157@1HD1 idatm_type HC
atom id /A:157@2HD1 idatm_type HC
atom id /A:157@3HD1 idatm_type HC
atom id /A:157@1HD2 idatm_type HC
atom id /A:157@2HD2 idatm_type HC
atom id /A:157@3HD2 idatm_type HC
atom id /A:158@N idatm_type Npl
atom id /A:158@CA idatm_type C3
atom id /A:158@C idatm_type C2
atom id /A:158@O idatm_type O2
atom id /A:158@CB idatm_type C3
atom id /A:158@CG idatm_type C3
atom id /A:158@CD idatm_type Cac
atom id /A:158@OE1 idatm_type O2-
atom id /A:158@OE2 idatm_type O2-
atom id /A:158@H idatm_type H
atom id /A:158@HA idatm_type HC
atom id /A:158@1HB idatm_type HC
atom id /A:158@2HB idatm_type HC
atom id /A:158@1HG idatm_type HC
atom id /A:158@2HG idatm_type HC
atom id /A:159@N idatm_type Npl
atom id /A:159@CA idatm_type C3
atom id /A:159@C idatm_type C2
atom id /A:159@O idatm_type O2
atom id /A:159@CB idatm_type C3
atom id /A:159@CG1 idatm_type C3
atom id /A:159@CG2 idatm_type C3
atom id /A:159@CD1 idatm_type C3
atom id /A:159@H idatm_type H
atom id /A:159@HA idatm_type HC
atom id /A:159@HB idatm_type HC
atom id /A:159@1HG1 idatm_type HC
atom id /A:159@2HG1 idatm_type HC
atom id /A:159@1HG2 idatm_type HC
atom id /A:159@2HG2 idatm_type HC
atom id /A:159@3HG2 idatm_type HC
atom id /A:159@1HD1 idatm_type HC
atom id /A:159@2HD1 idatm_type HC
atom id /A:159@3HD1 idatm_type HC
atom id /A:160@N idatm_type Npl
atom id /A:160@CA idatm_type C3
atom id /A:160@C idatm_type C2
atom id /A:160@O idatm_type O2
atom id /A:160@CB idatm_type C3
atom id /A:160@CG idatm_type C3
atom id /A:160@CD1 idatm_type C3
atom id /A:160@CD2 idatm_type C3
atom id /A:160@H idatm_type H
atom id /A:160@HA idatm_type HC
atom id /A:160@1HB idatm_type HC
atom id /A:160@2HB idatm_type HC
atom id /A:160@HG idatm_type HC
atom id /A:160@1HD1 idatm_type HC
atom id /A:160@2HD1 idatm_type HC
atom id /A:160@3HD1 idatm_type HC
atom id /A:160@1HD2 idatm_type HC
atom id /A:160@2HD2 idatm_type HC
atom id /A:160@3HD2 idatm_type HC
atom id /A:161@N idatm_type Npl
atom id /A:161@CA idatm_type C3
atom id /A:161@C idatm_type Cac
atom id /A:161@O idatm_type O2-
atom id /A:161@OXT idatm_type O2-
atom id /A:161@H idatm_type H
atom id /A:161@1HA idatm_type HC
atom id /A:161@2HA idatm_type HC

addcharge sel

Using Amber 20 recommended default charges and atom types for standard residues

color byattribute charge fiveA

557 atoms, 33 residues, 1 surfaces, atom charge range -0.819 to 0.805

show #1.1 models

hide #1.1 models

show #1.1 models

hide #1.1 models

show #1.2 models

hide #1.2 models

show #1.2 models

sle clear

Unknown command: sle clear

select clear

distance 135 162

Missing or invalid "objects" argument: invalid objects specifier

distance /A:135 /B162

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 16 atoms and 0 measurable objects

distance /A:135 /B:162

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 59 atoms and 0 measurable objects

Unknown command: sequence /A

Unknown command: sequence A

#1/A

Unknown command: sequence #1/A

Unknown command: sequence #1

select /A

2928 atoms, 2936 bonds, 161 residues, 1 model selected

Incomplete command: sequence

Unknown command: sequence /A

version

UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.

sequence chain #1/A

Alignment identifier is 1/A

save "C:\Users\moham\Downloads\Chimera Testing Grounds\#3A.png"

select /B :< 4 & ~/B

423 atoms, 405 bonds, 26 residues, 1 model selected

color all yellow

select /B :< 4 & ~/B

423 atoms, 405 bonds, 26 residues, 1 model selected

name frozen fourA

Missing or invalid "objects" argument: empty atom specifier

name frozen sel fourA

Missing or invalid "objects" argument: invalid objects specifier

name frozen fourA sel

select clear

select fourA

2928 atoms, 405 bonds, 161 residues, 1 model selected

name remove fourA

select /B :< 4 & ~/B

423 atoms, 405 bonds, 26 residues, 1 model selected

select up

2628 atoms, 2631 bonds, 142 residues, 2 models selected

select up

2928 atoms, 2936 bonds, 161 residues, 2 models selected

select down

2628 atoms, 2631 bonds, 142 residues, 2 models selected

select down

423 atoms, 405 bonds, 26 residues, 2 models selected

name frozen fourA sel

color (#!1 & sel) blue

color byattribute charge fourA

423 atoms, 26 residues, 1 surfaces, atom charge range -0.819 to 0.805

save "C:\Users\moham\Downloads\Chimera Testing Grounds\#3B.png"

color fourA yellow

select /B :< 3.5 & ~/B

363 atoms, 347 bonds, 22 residues, 1 model selected

name frozen threehalfA sel

color threehalfA yellow

color byattribute charge threehalfA

363 atoms, 22 residues, 1 surfaces, atom charge range -0.819 to 0.805

save "C:\Users\moham\Downloads\Chimera Testing Grounds\#3C.png"

hide #!1 models

show #!1 models

hide /A

[Repeated 1 time(s)]

select /A

2928 atoms, 2936 bonds, 161 residues, 1 model selected

hide sel cartoons

select clear

select /B:162@C2

1 atom, 1 residue, 1 model selected

select /B:162@C8

1 atom, 1 residue, 1 model selected

select clear

[Repeated 1 time(s)]

select /B:162@C2

1 atom, 1 residue, 1 model selected

select /B:162@C8

1 atom, 1 residue, 1 model selected

select clear

select /B:162@C2

1 atom, 1 residue, 1 model selected

select /B:162@C8

1 atom, 1 residue, 1 model selected

select add /B:162@C2

2 atoms, 1 residue, 1 model selected

select add /B:162@C9

3 atoms, 1 residue, 1 model selected

select add /B:162@C11

4 atoms, 1 residue, 1 model selected

torsion

Missing or invalid "atoms" argument: empty atom specifier

torsion sel

Torsion angle for atoms /B HBC 162 C8 C2 C9 C11 is 6.36484°

select 107

Expected an objects specifier or a keyword

select :107

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

color byattribute charge

2971 atoms, 162 residues, 1 surfaces, atom charge range -0.919 to 0.819

show sel cartoons

[Repeated 1 time(s)]

hide sel cartoons

select /A

2928 atoms, 2936 bonds, 161 residues, 1 model selected

show sel cartoons

undo

[Repeated 5 time(s)]

"Unable to open monitor interface to \\\\.\\DISPLAY1:" "Unknown error 0xe0000225."

[Repeated 17 time(s)]

[Repeated 3 time(s)]

[Repeated 3 time(s)]

[Repeated 3 time(s)]

[Repeated 9 time(s)]

[Repeated 5 time(s)]

select fiveA

2928 atoms, 536 bonds, 161 residues, 1 model selected

select forA

Expected an objects specifier or a keyword

select fourA

2928 atoms, 405 bonds, 161 residues, 1 model selected

show sel cartoons

select threehalfA

2928 atoms, 347 bonds, 161 residues, 1 model selected

select /B :< 4 & ~/B

423 atoms, 405 bonds, 26 residues, 1 model selected

name frozen fourA

Missing or invalid "objects" argument: empty atom specifier

name frozen fourA sel

select fiveA

2928 atoms, 536 bonds, 161 residues, 1 model selected

select fourA

2928 atoms, 405 bonds, 161 residues, 1 model selected

select up

2971 atoms, 2981 bonds, 162 residues, 2 models selected

select up

2971 atoms, 2981 bonds, 162 residues, 3 models selected

select up

2971 atoms, 2981 bonds, 162 residues, 3 models selected

select down

2 models selected

select down

Nothing selected

select /B :< 4 & ~/B

423 atoms, 405 bonds, 26 residues, 1 model selected

name frozen fourA sel

select fourA

2928 atoms, 405 bonds, 161 residues, 1 model selected

select ~sel & ##selected

43 atoms, 45 bonds, 1 residue, 1 model selected

select up

2971 atoms, 2981 bonds, 162 residues, 1 model selected

select up

2971 atoms, 2981 bonds, 162 residues, 3 models selected

select down

2971 atoms, 2981 bonds, 162 residues, 2 models selected

select down

43 atoms, 45 bonds, 1 residue, 2 models selected

select up

2971 atoms, 2981 bonds, 162 residues, 1 model selected

select up

2971 atoms, 2981 bonds, 162 residues, 3 models selected

select down

2971 atoms, 2981 bonds, 162 residues, 2 models selected

select down

43 atoms, 45 bonds, 1 residue, 2 models selected

select /B

43 atoms, 45 bonds, 1 residue, 1 model selected

select /B :< 4 & ~/B

423 atoms, 405 bonds, 26 residues, 1 model selected

name frozen sel fourA

"sel" is reserved and cannot be redefined

name frozen fourA sel

select fourA

2928 atoms, 405 bonds, 161 residues, 1 model selected

name list

fiveA [557 atoms, 1072 bonds, 2 models]
fourA [423 atoms, 810 bonds, 2 models]
remove fourA
threehalfA [363 atoms, 694 bonds, 2 models]

select fiveA

2928 atoms, 536 bonds, 161 residues, 1 model selected

info selection

select "fiveA"

2928 atoms, 536 bonds, 161 residues, 1 model selected

select fiveA

2928 atoms, 536 bonds, 161 residues, 1 model selected

alias list

select fiveA

2928 atoms, 536 bonds, 161 residues, 1 model selected

info models

model id #1 type AtomicStructure name wFAP0.pdb
model id #1.1 type MolecularSurface name "wFAP0.pdb_A SES surface"
model id #1.2 type ObjectLabels name labels

name list

fiveA [557 atoms, 1072 bonds, 2 models]
fourA [423 atoms, 810 bonds, 2 models]
remove fourA
threehalfA [363 atoms, 694 bonds, 2 models]

color red fiveA

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword

select :1-5

87 atoms, 86 bonds, 5 residues, 1 model selected

name test sel

select clear

seldct test

Unknown command: seldct test

select test

Nothing selected

select /A:2-17

289 atoms, 288 bonds, 16 residues, 1 model selected

select /A:2-28

491 atoms, 490 bonds, 27 residues, 1 model selected