User:Angel Herraez/Sandbox 8

==Dihedral angles (ϕ and ψ) in proteins and Ramachandran plot==

<table>

<tr>

<th>Structure

</th>

<th style="text-align:left;"><span style="width:380px; text-align:center; display:inline-block;">Ramachandran plot</span>

</th>

</tr>

<tr>

<td style="padding-right:1ex; vertical-align:top;">

<jmol>

<jmolApplet>

<size>450</size>

<color>white</color>

<uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents>

<script>

r_k = 35;

moveto 0 {426 -575 698 151.19} 85 0 0 {109.5 -2.1 -4.584} 7.74 {0 0 0} 0 0 0 3 0 0;

define r_m resNo=@{r_k-1}; define r_n resNo=@{r_k}; define r_o resNo=@{r_k+1};

define r_nN r_n and *.N; define r_nC r_n and *.C; define r_nO r_n and *.O;

define r_nH r_n and *.H; define r_nCA r_n and *.CA;

</script>

<!--script>

set echo values 50 100%; echo φ= @{format("%0.0f",{r_n}.phi)} |ψ= @{format("%0.0f",{r_n}.psi)}; refresh;

function toPhi(n) {

define tmp selected;

select r_m, r_nN, r_nH;

rotateSelected {r_nCA} {r_nN} @{n - {r_n}.phi}; calculate structure;

select tmp;

};

function toPsi(n) {

define tmp selected;

select r_nC, r_nO, r_o;

rotateSelected {r_nCA} {r_nC} @{n - {r_n}.psi}; calculate structure;

select tmp;

};

javascript fromStructToRama(true);

</script-->

</jmolApplet>

</jmol>

</td>

<td>

<div style="float:left; margin-right:1ex;">

<div style="width:380px; text-align:center; font-size:0.9em; padding:0 0 4px 0;">(drag the purple point around)

</div>

<div id="rama" style="width:380px; height:380px; position:relative; border:1px solid gray;">

<div id="hCont"></div>

<div id="vCont"></div>

<div id="axisY"></div>

<div id="axisX"></div>

<div id="axisXlabel">&#x03D5;</div>

<div id="axisYlabel">&#x03C8;</div>

<div id="ramaPoint" class="draggable" data-x="180" data-y="180"></div>

</div>

</div>

<p><span class="greek">&#x03D5;</span> = phi ;

<span class="greek">&#x03C8;</span> = psi

</p>

<div class="sideOpts">

While dragging in the plot, restrict to:<br>

<span><input type="radio" name="fixAng" onClick="fix_a(0)" id="freeA" checked>none </span>

<span><input type="radio" name="fixAng" onClick="fix_a('phi')">constant phi </span>

<span><input type="radio" name="fixAng" onClick="fix_a('psi')">constant psi </span>

</div>

<div class="sideOpts">Or enter values:<br>

<span style="padding-right:1ex;"><span class="greek">&#x03D5;</span> =

<input type="text" id="phi_V" style="width:4.5ex;"></span>

<span><span class="greek">&#x03C8;</span> =

<input type="text" id="psi_V" style="width:4.5ex;"></span>

<span><input type="button" value="apply" onClick="setStruct()"></span>

</div>

<div class="sideOpts">

Structure rotation changing one angle:<br>

<button onClick="rotate('phi');return false;"><span class="greek">&#x03D5;</span> play/pause</button>

<button onClick="rotate('psi');return false;"><span class="greek">&#x03C8;</span> play/pause</button>

</div>

<div class="sideOpts">

<input type="checkbox" id="bumps">

<span style="border-bottom:3px solid magenta;border-top:3px solid magenta;">Highlight</span> collisions or clashes <br>

(steric hindrance) <div class="Estilo1">(does not work during rotation)</div>

</div>

<div id="ramaLegend" style="clear:both; padding-top:0.3em;">

<p>Legend for Ramachandran plot:

</p>

<ul>

<li><span class="line" style="border-style:solid;"></span> boundary of rather stable conformations (favoured) </li>

<li><span class="line" style="border-style:dashed;"></span> boundary of moderately stable conformations (allowed) </li>

<li><b><span class="greek">&alpha;</span></b> alpha helix (right-handed, the usual one)</li>

<li><b>L<span class="greek">&alpha;</span></b> left-handed alpha helix (less common)</li>

<li><b>3₁₀</b> 3_10 helix</li>

<li><b>&beta;</b> beta strand, beta sheet</li>

<li><b>poly P</b> polyproline helix (also collagen)</li>

</ul>

</div>

</td>

</tr>

</table>

<p style="font-size:0.8em; color:gray;">

Image of Ramachandran plot areas modified from &#8220;[https://commons.wikimedia.org/wiki/File%3ARamachandran_plot_original_outlines.jpg|Ramachandran_plot_original_outlines]&#8221; by Dcrjsr [CC-BY license]

</p>