Talk:Kisker lab: 5B5Q

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Revision as of 15:22, 16 March 2018 (edit) Karsten Theis (Talk | contribs) ← Previous diff		Revision as of 19:25, 16 March 2018 (edit) (undo) Karsten Theis (Talk | contribs) (→Scripts used) Next diff →
Line 60:		Line 60:
	Bonus:		Bonus:
-	<nowiki>select all	+	<nowiki>select all; cartoon only; color silver
-	cartoon only	+	select 275,292,345 and sidechain; wireframe 0.3
-	color silver	+	select 345 and sidechain; color yellow
-	select 275,292,345 and sidechain	+
-	wireframe 0.3	+
-	select 345 and sidechain	+
-	color yellow	+
	center selected		center selected
	select protein and within(10.0, 271) and not 249-273		select protein and within(10.0, 271) and not 249-273
-	isosurface ignore(solvent or 249-273) molecular MAP property color	+	isosurface ignore(not selected) molecular MAP property color
-	select 254-270	+	select 254-270; trace only; color yellow
-	trace only	+	select 271 and (sidechain or *.CA) and _C; wireframe 0.5
-	color skyblue	+	select 271.CB; label "%r%n"; color label black</nowiki>
-	select 271 and (sidechain or *.CA) and _C	+
-	wireframe 0.5</nowiki>	+

---

Revision as of 19:25, 16 March 2018

Scripts used

Panel A:

select all; cartoon only; color yellowgreen
select 249-273; color yellow
select (275,292,345) and (*.CA or sidechain) and not hydrogen; wireframe .3;
select selected and not *.CA; color cpk

Panel B:

load 1EUV
select :A
color skyblue
select :B
color orange
select 511-513
color yellow
cartoon 0.3

Panel C:

load 1XT9
cartoon only
select :A
color white
select :B
color mediumorchid
select 92-102
color yellow
cartoon 0.3
set zshade on
set zshadepower 2

Panel D:

select all; cartoon only; color yellow
select (275,292,345) and not hydrogen; wireframe .3;
select selected and not _C; color cpk
select (275,292,345) and *.SG; color goldenrod
set zshade on
set zshadepower 2

Panel E:

sselect all; cartoon only; color silver
select :B/2; hide selected

# color CDUB1 like panel A and show catalytic triad
select :a/2; color lime
select 249-273; color yellow
select (275,345,292) and (sidechain or *.CA) and not _H; wireframe 100%
select selected and not _C; color CPK

# color the related deubiquitinase like panel C
select :B/1; color orchid
select 70-76:B/1; wireframe only; wireframe 100%
select selected and not _C; color CPK
select (102:A/1, 163:A/1, 119:A/1) and (sidechain or *.CA) and not _H; wireframe 100%
select selected and not _C; color CPK

# add the covelent enzyme-substrate bond
select 76:B.C,163.SG; connect 1.9 (selected)(selected); wireframe 100%

Bonus:

select all; cartoon only; color silver
select 275,292,345 and sidechain; wireframe 0.3
select 345 and sidechain; color yellow
center selected
select protein and within(10.0, 271) and not 249-273
isosurface ignore(not selected) molecular MAP property color
select 254-270; trace only; color yellow
select 271 and (sidechain or *.CA) and _C; wireframe 0.5
select 271.CB; label "%r%n"; color label black