Talk:Hen Egg-White (HEW) Lysozyme

From Proteopedia

Revision as of 15:31, 16 July 2019

List of green links and interactive features

C:\Users\ktheis\AppData\Local\Programs\Python\Python38\python.exe C:/Users/ktheis/PycharmProjects/JmolSel/mine_proteopedia.py
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