User:Karsten Theis/AI tutorial: Difference between revisions

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Editor, Macro, Print3D
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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
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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' />
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Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well).
Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well).


The initial scene: Chymotrypsin active site
The <scene name='85/857774/Chymotrypsin/4'>initial scene</scene>: Chymotrypsin active site
 


  <nowiki>
  <nowiki>
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</nowiki>
</nowiki>


<scene name='78/786673/Nagal_galsa_superposition/1'>Superposition</scene>
<scene name='10/1076814/Etransfer/1'>Electron transfer</scene>
 
<nowiki>
load "=1JRO" filter "biomolecule 2"                                  # The structure contains 2 dimers, we are loading the second dimer
restrict none
define ~focal FES:E, FAD:E, MTE:F, MOS:F                              # Ligands involved in electron transfer (in chain E, F, not G, H)
select (sulfur and MTE:F) or MOS:E.MO; bondOrder single              # show bond between sulfur atoms and molybdenum
select ~focal; wireframe 0.36; Spacefill 25%                          # ball-and-stick (atom colors default to CPK upon loading)
select 3001:E.S2 or 3002:E.FE1; label "Fe2S2"; color label [xffa500]; # label electron carriers
select FAD:E.O2; label "FAD"                                          # label electron donor (color as atom)
select MOS:F.MO; label "MoCo"                                        # label electron acceptor (color as atom)
select ~focal; set labelOffset 4 4;                                  # offset for all labels
center visible; zoom 400; spin on                                    # there is no good single view, so spin
set measurementUnits Angstroms                                        # units for the measurements below
measure ([FAD]3005:E.C7M) ([FES]3002:E.S1)                            # shortest path for electrons
measure ([FES]3002:E.FE2) ([FES]3001:E.S2)
measure ([FES]3001:E.FE1) ([MTE]3003:F.C2)
</nowiki>
 
 
<scene name='80/804504/Dna/5'>Base stacking</scene>
 
 
<nowiki>
load =4c64
restrict none
define ~focal [DC]21:B or [DG]4:A                                      # G:C base pair
select ~focal; wireframe 0.3;                                          # show entire nucleotide (with backbone)
select sidechain and 5:A, 3:A, 20:B, 22:B; wireframe 0.2; color gray  # stacking G:C and A:T base pair, just nucleobases
select 20:B or 5:A; color atoms opaque [xff7f50]; # coral              # A:T base pair in coral
 
# The following shows the focal base pair as surface, with coloring indicating distance of closest stacked atom
set defaultVDW JMOL                                                    # sets Van der Waals radii
contact ID "contact1" ({(21:B or 4:A) and sidechain}) ({sidechain and (5:A, 3:A, 20:B ,22:B)}) surface;
contact ID "contact1" fill noMesh noDots notFrontOnly frontlit;        # surface representation parameters
color $"contact1""roygb" range -0.5 1;                                # color scheme rainbow, with overlap in VdW radii in red
 
# Here is how to find the neighboring nucleobases (which are given explicitly in the "contact" command above)
# select within(3.8, ~focal and sidechain) and not (~focal or water)
# define ~neighbors within(group, selected) and sidechain
 
center visible; zoom 250
 
</nowiki>
 
 
<scene name='10/1076814/Intercalation/1'>Intercalation</scene>
 
<nowiki>
load =3k5y                                                                # RNA bound to protein
restrict none
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;    # entire side chain plus alpha carbon shown
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                                    # entire protein shown as thin backbone
select RNA and sidechain; Spacefill 100%; color atoms red;                # Nucleobases shown as red spacefilling (this is the focus of the figure)
select RNA and mainchain; Spacefill 0.5;                                  # rest of RNA shown as ball...
select RNA; wireframe 0.3;                                                # and stick (it's fine to show nucleobases as wireframe, too, gets occluded)
center RNA; zoom 200                                                      # center of rotation is RNA so it stays in view
</nowiki>
 
<scene name='10/1076814/Nagal_galsa_superposition/1'>Superposition</scene>
 


<jmol>
<jmol>
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compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE                # superposition (different sequences, so use alpha carbon)
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE                # superposition (different sequences, so use alpha carbon)
set ssbonds SIDECHAIN                                                                # disulfide bonds are anchored on SG, not on CA
set ssbonds SIDECHAIN                                                                # disulfide bonds are anchored on SG, not on CA
set traceAlpha TRUE
set zshade on
set sheetSmoothing 0.3


# drawing 3H54 active site
# drawing 3H54 active site
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color bonds yellow                                                                    # 3LX9 is shown in yellow (just the bonds)
color bonds yellow                                                                    # 3LX9 is shown in yellow (just the bonds)
select selected and not _C; spacefill 80; color cpk                                  # spacefill, atoms other than carbon shown using CPK color scheme
select selected and not _C; spacefill 80; color cpk                                  # spacefill, atoms other than carbon shown using CPK color scheme
select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA;# some main chain context for the active site residues
select 2.1 and (46-48, 91-94, 133-135, 141-143, 167-173, 202-208, 226-232) and *:A.CA;# some main chain context for the active site residues
trace 10; color yellow                                                                # show as trace in yellow  
trace 10; color yellow                                                                # show as trace in yellow  
select 2.1 and 1000:A; wireframe 60;;                                                # selecting the sugar in 3LX9  
select 2.1 and 1000:A; wireframe 60;;                                                # selecting the sugar in 3LX9  
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</nowiki>
</nowiki>


<scene name='10/100139/Spacefill/1'>Green fluorescent protein</scene>
<nowiki>
load =1ema
# 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>




===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                                        # UvrB, a helicase-like protein bound to ATP
restrict none
select protein; color gold; cartoon on            # The gold domain has most segments, so make everything gold
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 91-116; color aqua                        # beta hairpin, unique to UvrB
select 245-324, 349-378; color lime              # UvrA interaction domain
select MG, ATP, ZN; color silver; spacefill 100%  # Ligands in spacefill (Zn is crystallization artifact)
</nowiki>
<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>
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