User:Karsten Theis/AI tutorial - Revision history

Karsten Theis at 18:05, 8 May 2025

2025-05-08T18:05:53Z

← Older revision		Revision as of 18:05, 8 May 2025
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	This is a tutorial for AI how to help with making 3D figures in Jmol. If it helps humans too, so much the better.		This is a tutorial for AI how to help with making 3D figures in Jmol (see all materials [https://github.com/ktheis/Jmol-Jane here]). If it helps humans too, so much the better.

	<Structure load='' size='350' frame='true' align='right' caption='' scene='85/857774/Chymotrypsin/4' />		<Structure load='' size='350' frame='true' align='right' caption='' scene='85/857774/Chymotrypsin/4' />

2025-04-15T17:24:07Z

← Older revision		Revision as of 17:24, 15 April 2025
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	<nowiki>		<nowiki>
	load =~~1edm~~		load =1ema
	# define the central helix in GFP and the hydrophobic residues lining it		# define the central helix in GFP and the hydrophobic residues lining it
	define ~helix 57-71		define ~helix 57-71

2025-04-15T17:00:43Z

← Older revision		Revision as of 17:00, 15 April 2025
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	</nowiki>		</nowiki>

	<scene name='10/100139/Spacefill/1~~.spt~~'>Green fluorescent protein</scene>		<scene name='10/100139/Spacefill/1'>Green fluorescent protein</scene>

	<nowiki>		<nowiki>

2025-04-15T16:58:52Z

← Older revision		Revision as of 16:58, 15 April 2025
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	</nowiki>		</nowiki>

	<scene name='~~https://proteopedia.org/wiki/scripts/~~10/100139/Spacefill/1.spt'>Green fluorescent protein</scene>		<scene name='10/100139/Spacefill/1.spt'>Green fluorescent protein</scene>

	<nowiki>		<nowiki>

2025-04-15T16:56:35Z

← Older revision		Revision as of 16:56, 15 April 2025
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	</nowiki>		</nowiki>

			<scene name='https://proteopedia.org/wiki/scripts/10/100139/Spacefill/1.spt'>Green fluorescent protein</scene>

			<nowiki>
			load =1edm
			# define the central helix in GFP and the hydrophobic residues lining it
			define ~helix 57-71
			define ~hydrophobic_liner 12, 14, 16, 18, 22, 27, 29, 42, 44, 46, 48, 98, 100, 110, 112, 114, 119, 123, 125, 150, 152, 161, 163, 165, 167, 179, 201, 207, 220, 224, 226

			# Show a translucent ribbon for context (some of the colors are overridden later)
			select all
			Ribbon on;
			color atoms translucent 128 [xf0f8ff]; # aliceblue

			# The helix is shown as solid red spacefill
			select ~helix
			Spacefill 100%
			color atoms opaque [xdc143c]; # crimson

			# The side chains lining it are shown as solid whitish spacefill
			select sidechain and ~hydrophobic_liner
			color atoms opaque [xf0f8ff]; # aliceblue
			Spacefill 100%
			</nowiki>

2025-04-04T02:53:24Z

← Older revision		Revision as of 02:53, 4 April 2025
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	<scene name='10/1071246/Trypsin_5mop/5'>Rainbow plus surface</scene>		<scene name='10/1071246/Trypsin_5mop/5'>Rainbow plus surface</scene>

			<nowiki>
			load =5mop # trypsin
			restrict none
			select protein; cartoon on; color group # rainbow cartoon
			select protein and (57,195) and sidechain and not hydrogen; color cpk; spacefill 25% # ball ...
			select protein and (57,195) and (sidechain or alpha) and not hydrogen; wireframe 0.36 # ...and stick
			select protein; isosurface ID "1" SASURFACE # solvent-accessible surface
			color isosurface translucent 0.875 white # white and translucent
			isosurface ID "1" fill noMesh noDots notFrontOnly frontlit # these settings help to see the cartoon
			select all; set hoverLabel "%n %R"; # residue numbers and name
			select [CA]; set hoverLabel "Calcium"; # spell out "calcium" to distinguish from alpha-carbon
			</nowiki>

2025-04-03T21:20:36Z

← Older revision		Revision as of 21:20, 3 April 2025
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	select MG, ATP, ZN; color silver; spacefill 100% # Ligands in spacefill (Zn is crystallization artifact)		select MG, ATP, ZN; color silver; spacefill 100% # Ligands in spacefill (Zn is crystallization artifact)
	</nowiki>		</nowiki>


			<scene name='10/1071246/Trypsin_5mop/5'>Rainbow plus surface</scene>

2025-04-03T21:16:50Z

← Older revision		Revision as of 21:16, 3 April 2025
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	<nowiki>		<nowiki>
	load =1d9z		load =1d9z # UvrB, a helicase-like protein bound to ATP
	restrict none		restrict none
	select protein; color gold; cartoon on		select protein; color gold; cartoon on # The gold domain has most segments, so make everything gold
	select 415-595; color red		select not helix and not sheet; cartoon 0.3 # Make coils a bit thicker than default for balance and visibility
			select 415-595; color red
	select 157-244; color blue		select 157-244; color blue
	select 91-116; color aqua		select 91-116; color aqua # beta hairpin, unique to UvrB
	select 245-324, 349-378; color lime		select 245-324, 349-378; color lime # UvrA interaction domain
	select MG, ATP, ZN; color silver; spacefill 100%		select MG, ATP, ZN; color silver; spacefill 100% # Ligands in spacefill (Zn is crystallization artifact)
	~~select not helix and not sheet; cartoon 0.3~~
	</nowiki>		</nowiki>

2025-04-03T19:30:13Z

← Older revision		Revision as of 19:30, 3 April 2025
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	===Overall views===		===Overall views===
	These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back.		These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back.


			<scene name='78/780454/Domains/7'>Domains</scene>

			<nowiki>
			load =1d9z
			restrict none
			select protein; color gold; cartoon on
			select 415-595; color red
			select 157-244; color blue
			select 91-116; color aqua
			select 245-324, 349-378; color lime
			select MG, ATP, ZN; color silver; spacefill 100%
			select not helix and not sheet; cartoon 0.3
			</nowiki>

2025-04-03T19:09:30Z

← Older revision		Revision as of 19:09, 3 April 2025
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	<scene name='80/~~804504~~/Intercalation/2'>Intercalation</scene>		<scene name='10/1076814/Intercalation/1'>Intercalation</scene>

	<nowiki>		<nowiki>
	load =3k5y		load =3k5y # RNA bound to protein
	restrict none		restrict none
	select protein and sidechain and within(3.5, RNA and sidechain);		select protein and sidechain and within(3.5, RNA and sidechain); # protein side chain atoms that are close to nucleobases
	select within(group, selected) and (alpha or sidechain); wireframe 0.3;		select within(group, selected) and (alpha or sidechain); wireframe 0.3; # entire side chain plus alpha carbon shown
	select selected and (alpha or *.CB); color bond gray;		select selected and (alpha or *.CB); color bond gray; # fix bond color between alpha and beta carbon to uniform gray
	select alpha; backbone on; color chain		select alpha; backbone on; color chain # entire protein shown as thin backbone
	~~select RNA; wireframe 0.3;~~		select RNA and sidechain; Spacefill 100%; color atoms red; # Nucleobases shown as red spacefilling (this is the focus of the figure)
	select RNA and sidechain; Spacefill 100%; color atoms red;		select RNA and mainchain; Spacefill 0.5; # rest of RNA shown as ball...
	select RNA and mainchain; Spacefill 0.5;		select RNA; wireframe 0.3; # and stick (it's fine to show nucleobases as wireframe, too, gets occluded)
	center RNA; zoom 200		center RNA; zoom 200 # center of rotation is RNA so it stays in view
	</nowiki>		</nowiki>