User:Angel Herraez/Sandbox 8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(Test of mmCIF assemblies)
Line 1: Line 1:
-
== Test of mmCIF assemblies ==
+
==Dihedral angles (ϕ and ψ) in proteins and Ramachandran plot==
-
<StructureSection load='1xxx_1' size='350' side='right' caption='assembly of PDB entry 1xxx' scene=''>
+
<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>3<sub>10</sub></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>
-
Load the page. The file is 1xxx_1.gz
 
-
The echo shows "simplifed model" -- OK
+
<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]
-
Try this:
+
</p>
-
console
+
-
select protein and not alpha
+
-
 
+
-
0 atoms selected (meaning it's indeed the simplified model) -- OK
+
-
 
+
-
Now click on "load full" button
+
-
 
+
-
the echo dissapears
+
-
 
+
-
console
+
-
select protein and not alpha
+
-
 
+
-
7354 atoms selected -- OK, we have the full model
+
-
 
+
-
 
+
-
</StructureSection>
+
-
 
+
-
 
+
-
== References ==
+
-
<references/>
+

Revision as of 22:02, 19 July 2016

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

Structure Ramachandran plot
Drag the structure with the mouse to rotate
(drag the purple point around)
ϕ
ψ

ϕ = phi ; ψ = psi

While dragging in the plot, restrict to:
<input type="radio" name="fixAng" onClick="fix_a(0)" id="freeA" checked>none <input type="radio" name="fixAng" onClick="fix_a('phi')">constant phi <input type="radio" name="fixAng" onClick="fix_a('psi')">constant psi

Or enter values:

ϕ = <input type="text" id="phi_V" style="width:4.5ex;"> ψ = <input type="text" id="psi_V" style="width:4.5ex;"> <input type="button" value="apply" onClick="setStruct()">

Structure rotation changing one angle:
<button onClick="rotate('phi');return false;">ϕ play/pause</button> <button onClick="rotate('psi');return false;">ψ play/pause</button>

<input type="checkbox" id="bumps"> Highlight collisions or clashes

(steric hindrance)
(does not work during rotation)

Legend for Ramachandran plot:

  • boundary of rather stable conformations (favoured)
  • boundary of moderately stable conformations (allowed)
  • α alpha helix (right-handed, the usual one)
  • Lα left-handed alpha helix (less common)
  • 310 3_10 helix
  • β beta strand, beta sheet
  • poly P polyproline helix (also collagen)


Image of Ramachandran plot areas modified from “[1]” by Dcrjsr [CC-BY license]

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez

Retrieved from "http://52.214.119.220/wiki/index.php/User:Angel_Herraez/Sandbox_8"
Personal tools