Talk:Hen Egg-White (HEW) Lysozyme
From Proteopedia
How some of the figures were made
Opening scene:
This is a script to create the opening scene after loading coordinate 1HEW (you could also use the screen authoring tool)
restrict none #clean slate select ligand; wireframe 0.3; spacefill 0.5; #make bonds on ligand a bit thicker select protein; backbone 0.4; color backbone group #rainbow c-alpha trace color background black #as it says select *.CA; spacefill 0.8; #spheres on alpha carbons label "%m";set labelOffset 0 0; color label yellow #...with yellow labels on top hover "%n %r, Chain=%c, Element=%e"; #show 3-letter code number, chain and element select cys.sg; wireframe 0.25; set ssbonds backbone #disulfide bonds
Here is an animation to see what the commands do [Image:Lysozyme commands.gif]]
and a screen shot of the finished scene with captions for reference
List of green links and interactive features
This is an overview of Jmol features on the page, --Karsten Theis 15:33, 16 July 2019 (UTC)
Scripts from https://proteopedia.org/wiki/index.php/Lysozyme
Initial view
https://proteopedia.org/wiki/scripts/37/376372/Overall/3.spt
Overview of the 1HEW structure. The trace of the protein chain is shown in rainbow colors with the alpha carbons as gray spheres labeled with the residue one letter code. The carbohydrate ligand is shown as ball and stick in CPK colors (carbon: gray, oxygen: red, nitrogen: blue).
reloads only when necessary
coordinates: https://proteopedia.org/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66
ribbon view
https://proteopedia.org/wiki/scripts/37/376372/Secondary_structure/7.spt
Overview of the 1HEW secondary structure: <font color="#f08">Alpha Helices</font>, <font color="#907">3-10 helix</font>, <font color="#ca0">Beta Strands</font>, with loops in white and disulfide bonds in yellow. Arrow tips point towards the C-terminal end.
reloads only when necessary
coordinates are those used for Initial view
colored by conservation
https://proteopedia.org/wiki/ConSurf/he/1hew_consurf.spt
coordinates downloaded: none
helices
https://proteopedia.org/wiki/scripts/37/376372/Hbonds/1.spt
Hydrogen bonding. Selected hydrogen bonds are shown as red dashed lines connecting the hydrogen bond acceptor and donor (hydrogen atoms not shown). The protein backbone is show as thick wireframe and the side chains as thin wireframe. Magenta: helices, gold: beta strands. The ligand is shown as ball-and-stick with purple carbons. Click on atoms to recenter the view.
reloads only when necessary
coordinates are those used for Initial view
beta turns
https://proteopedia.org/wiki/scripts/37/376372/Hbonds/5.spt
Hydrogen bonding. Selected hydrogen bonds are shown as red dashed lines connecting the hydrogen bond acceptor and donor (hydrogen atoms not shown). The protein backbone is show as thick wireframe and the side chains as thin wireframe. Magenta: helices, gold: beta strands. The ligand is shown as ball-and-stick with purple carbons. Click on atoms to recenter the view.
reloads only when necessary
coordinates are those used for Initial view
between strands
https://proteopedia.org/wiki/scripts/37/376372/Hbonds/2.spt
Hydrogen bonding. Selected hydrogen bonds are shown as red dashed lines connecting the hydrogen bond acceptor and donor (hydrogen atoms not shown). The protein backbone is show as thick wireframe and the side chains as thin wireframe. Magenta: helices, gold: beta strands. The ligand is shown as ball-and-stick with purple carbons. Click on atoms to recenter the view.
reloads only when necessary
coordinates are those used for Initial view
between protein and ligand
https://proteopedia.org/wiki/scripts/37/376372/Hbonds/3.spt
Hydrogen bonding. Selected hydrogen bonds are shown as red dashed lines connecting the hydrogen bond acceptor and donor (hydrogen atoms not shown). The protein backbone is show as thick wireframe and the side chains as thin wireframe. Magenta: helices, gold: beta strands. The ligand is shown as ball-and-stick with purple carbons. Click on atoms to recenter the view.
reloads only when necessary
coordinates are those used for Initial view
this hypothetical model
https://proteopedia.org/wiki/scripts/37/376372/Hex_model/1.spt
1HEW with additional three sugars modeled into the active site.
reloads only when necessary
coordinates: https://proteopedia.org/cgi-bin/getfrozenstructure?caa67c01c8140e2b3f7b60e4e749f1dd
covalent intermediate
https://proteopedia.org/wiki/scripts/37/376372/Covalent_intermediate/2.spt
Structure of the covalent enzyme intermediate. The active site residue Asp 52 and the carbohydrate are shown in CPK colors, with the 2FO-FC electron density within 1.5 A of these atoms as blue mesh. The backbone trace is shown in gold.
coordinates: https://proteopedia.org/cgi-bin/getfrozenstructure?932c10afc4e1e94cdeab12d300cbb47b
product complex with five sugar units
https://proteopedia.org/wiki/scripts/37/376372/Product_complex/6.spt
Comparison of covalent intermediate (1H6M) and product complex (2WAR), both for the almost inactive Glu35Gln mutant. Backbone in gold, with ligand in thick wireframe and side chains of active site residues 35 and 52 in thin wireframe. Fluorine is shown in green.
reloads only when necessary
coordinates: https://proteopedia.org/cgi-bin/getfrozenstructure?09a5df19589b9b4571d13eef460f52bf
Jmol commands: buttons etc
Lysozyme: jmolLink('script /scripts/37/376372/Overall/3.spt; hide water; set zshade off'...
☼: jmolLink(' select ligand; selectionHalos ON; delay 0.5;selectionHalos OFF;'...
☼: jmolLink(' select 1.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;'...
☼: jmolLink(' select 129.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;'...
☼: jmolLink(' select BONDS ({0:3}); wireframe 0.6; delay 0.5; wireframe 0.1'...
☼: jmolLink(' select helix and *.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;'...
☼: jmolLink(' select sheet and *.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;'...
Hydrophobic residues: jmolLink('select backbone or water; spacefill off; hide ligand or (sidechain and not (met, cys, ile, leu, val, phe, tyr, trp))'...
hydrophilic residues and proline: jmolLink('select backbone or water; spacefill off; hide ligand or (sidechain and (met, cys, ile, leu, val, phe, tyr, trp))'...
water: jmolLink('select backbone; spacefill on; select water; spacefill 1.0; display all'...
RadioGroup
hydrophobic side chains: hide (hidden and not sidechain) or (sidechain and not (met, cys, ile, leu, val, phe, tyr, trp))
hydrophilic side chains: hide (hidden and not sidechain) or (sidechain and (met, cys, ile, leu, val, phe, tyr, trp))
all side chains: display (displayed and not sidechain) or sidechain
RadioGroup
colored by hydrophobiticity: background white; select sidechain; color magenta; select sidechain and (cys, met, ile, leu, val, phe, tyr, trp); color gray; set echo ID bla 80% 0%; echo \"hydrophobic\"; color echo gray; frank off; set echo ID bla2 0% 0%; echo \"hydrophilic\"; color echo magenta
colored by charge: select sidechain; color white; select sidechain and (asp, glu); color red; select sidechain and (lys, arg, his); color blue; set echo ID bla 80% 0%; echo \"positive\"; color echo blue; frank off; set echo ID bla2 0% 0%; echo \"negative\"; color echo red
colored by conservation: select sidechain; define ~consurf_to_do selected; define ~consurf_to_color selected; useFullScript = true; consurf_initial_scene = false; script /wiki/ConSurf/he/1hew_consurf.spt; set echo ID bla 80% 0%; echo \"conserved\"; color echo firebrick; frank off; set echo ID bla2 0% 0%; echo \"variable\"; color echo darkturquoise
[± backbone spacefill]: jmolLink('if ({*.O and backbone and visible}.size\x3e0) {select backbone; spacefill off} else {select backbone; spacefill on} '...
[± ligand]: jmolLink('if ({ligand and hidden}.size\x3e0) {display displayed or ligand} else {hide ligand or hidden} '...
[± water]: jmolLink('if ({water and visible}.size\x3e0) {select water; spacefill off} else {select water; spacefill 1.0} '...
hydrogen bonds: jmolLink('set picking center; display all; script /scripts/37/376372/Hbonds/5.spt '...
Ordered waters: jmolLink('hide none; script /scripts/37/376372/Hbonds/4.spt '...
toggle fading and slabbing: jmolButton('if (zshade) {set zshade off; slab off} else {set zshade on; slab on}'...
turn centering on: jmolButton('set picking center'...
turn centering off: jmolButton('set picking identify'...
modeled extra sugars: jmolCheckbox('display all','hide 204-206'...
RadioGroup
product: anim off; delay 1.0; model 1
intermediate: anim off; delay 1.0; model 2
animate: anim fps 1; anim mode loop; anim on;
just ring: jmolCheckbox('hide ligand and not ((1134 or G2F) and (*.O1, *.C1, *.C2, *.C3, *.C4, *.C5, *.O5, *.N5, *.O4))','hide water'...
Total of green links: 10 and total of Jmol buttons etc: 23
