User:Angel Herraez/Sandbox 8

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Current revision (20:11, 30 September 2019) (edit) (undo)
(tests for tags of the JmolExtension)
 
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==Dihedral angles (&#x03D5; and &#x03C8;) in proteins and Ramachandran plot==
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== Test the extension ==
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<table>
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...This uses the inlineContents tag:
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<tr>
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<th>Structure
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</th>
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<th style="text-align:left;"><span style="width:380px; text-align:center; display:inline-block;">Ramachandran plot</span>
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</th>
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</tr>
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<tr>
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<td style="padding-right:1ex; vertical-align:top;">
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<jmol>
<jmol>
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<size>220</size>
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<color>#EEEEFF</color>
<jmolApplet>
<jmolApplet>
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<size>450</size>
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<inlineContents>
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<color>white</color>
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Menthol
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<uploadedFileContents>1iy4_34-36.pdb</uploadedFileContents>
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OpenBabel02151916433D
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<script>
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r_k = 35;
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31 31 0 0 0 0 0 0 0 0999 V2000
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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;
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0.6797 1.2651 -0.2387 C 0 0 0 0 0 0 0 0 0 0 0 0
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define r_m resNo=@{r_k-1}; define r_n resNo=@{r_k}; define r_o resNo=@{r_k+1};
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1.3944 -0.0096 0.2024 C 0 0 0 0 0 0 0 0 0 0 0 0
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define r_nN r_n and *.N; define r_nC r_n and *.C; define r_nO r_n and *.O;
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0.6695 -1.3027 -0.2371 C 0 0 2 0 0 0 0 0 0 0 0 0
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define r_nH r_n and *.H; define r_nCA r_n and *.CA;
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-0.8129 -1.2397 0.2137 C 0 0 1 0 0 0 0 0 0 0 0 0
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</script>
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-1.5089 0.0539 -0.2208 C 0 0 0 0 0 0 0 0 0 0 0 0
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<!--script>
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-0.7680 1.3033 0.2480 C 0 0 2 0 0 0 0 0 0 0 0 0
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set echo values 50 100%; echo φ= @{format("%0.0f",{r_n}.phi)} |ψ= @{format("%0.0f",{r_n}.psi)}; refresh;
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-1.4711 2.5652 -0.2509 C 0 0 0 0 0 0 0 0 0 0 0 0
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function toPhi(n) {
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-1.5752 -2.3115 -0.3340 O 0 0 0 0 0 0 0 0 0 0 0 0
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define tmp selected;
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1.4325 -2.5688 0.2868 C 0 0 0 0 0 0 0 0 0 0 0 0
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select r_m, r_nN, r_nH;
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0.7873 -3.8964 -0.1292 C 0 0 0 0 0 0 0 0 0 0 0 0
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rotateSelected {r_nCA} {r_nN} @{n - {r_n}.phi}; calculate structure;
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2.8961 -2.5942 -0.1835 C 0 0 0 0 0 0 0 0 0 0 0 0
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select tmp;
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1.2254 2.1343 0.1484 H 0 0 0 0 0 0 0 0 0 0 0 0
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};
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0.7117 1.3341 -1.3336 H 0 0 0 0 0 0 0 0 0 0 0 0
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function toPsi(n) {
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2.4050 0.0252 -0.2178 H 0 0 0 0 0 0 0 0 0 0 0 0
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define tmp selected;
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1.5013 -0.0027 1.2947 H 0 0 0 0 0 0 0 0 0 0 0 0
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select r_nC, r_nO, r_o;
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-1.6086 0.0630 -1.3151 H 0 0 0 0 0 0 0 0 0 0 0 0
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rotateSelected {r_nCA} {r_nC} @{n - {r_n}.psi}; calculate structure;
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-2.5371 0.0569 0.1639 H 0 0 0 0 0 0 0 0 0 0 0 0
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select tmp;
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0.6850 -1.3476 -1.3355 H 0 0 0 0 0 0 0 0 0 0 0 0
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};
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-0.8654 -1.3281 1.3056 H 0 0 0 0 0 0 0 0 0 0 0 0
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javascript fromStructToRama(true);
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-0.7714 1.3230 1.3457 H 0 0 0 0 0 0 0 0 0 0 0 0
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</script-->
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-1.4921 2.6034 -1.3455 H 0 0 0 0 0 0 0 0 0 0 0 0
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</jmolApplet>
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-0.9581 3.4631 0.1088 H 0 0 0 0 0 0 0 0 0 0 0 0
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-2.5048 2.6021 0.1085 H 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4957 -2.2720 -1.3025 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.4411 -2.5381 1.3844 H 0 0 0 0 0 0 0 0 0 0 0 0
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0.5863 -3.9212 -1.2054 H 0 0 0 0 0 0 0 0 0 0 0 0
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-0.1467 -4.0734 0.4111 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.4390 -4.7445 0.1088 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.9614 -2.5170 -1.2741 H 0 0 0 0 0 0 0 0 0 0 0 0
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3.3900 -3.5247 0.1184 H 0 0 0 0 0 0 0 0 0 0 0 0
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3.4778 -1.7803 0.2581 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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1 12 1 0 0 0 0
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1 13 1 0 0 0 0
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2 3 1 0 0 0 0
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2 14 1 0 0 0 0
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2 15 1 0 0 0 0
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3 4 1 1 0 0 0
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3 9 1 0 0 0 0
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3 18 1 0 0 0 0
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4 5 1 0 0 0 0
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4 8 1 0 0 0 0
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4 19 1 1 0 0 0
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5 6 1 0 0 0 0
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5 16 1 0 0 0 0
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5 17 1 0 0 0 0
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6 1 1 0 0 0 0
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6 7 1 0 0 0 0
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6 20 1 1 0 0 0
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7 21 1 0 0 0 0
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7 22 1 0 0 0 0
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7 23 1 0 0 0 0
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8 24 1 0 0 0 0
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9 10 1 0 0 0 0
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9 11 1 0 0 0 0
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9 25 1 0 0 0 0
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10 26 1 0 0 0 0
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10 27 1 0 0 0 0
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10 28 1 0 0 0 0
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11 29 1 0 0 0 0
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11 30 1 0 0 0 0
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11 31 1 0 0 0 0
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M END
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</inlineContents>
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</jmolApplet>
</jmol>
</jmol>
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</td>
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...end
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<td>
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<div style="float:left; margin-right:1ex;">
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<div style="width:380px; text-align:center; font-size:0.9em; padding:0 0 4px 0;">(drag the purple point around)
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</div>
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<div id="rama" style="width:380px; height:380px; position:relative; border:1px solid gray;">
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<div id="hCont"></div>
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<div id="vCont"></div>
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<div id="axisY"></div>
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<div id="axisX"></div>
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<div id="axisXlabel">&#x03D5;</div>
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<div id="axisYlabel">&#x03C8;</div>
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<div id="ramaPoint" class="draggable" data-x="180" data-y="180"></div>
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</div>
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</div>
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<p><span class="greek">&#x03D5;</span> = phi ;
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<span class="greek">&#x03C8;</span> = psi
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</p>
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<div class="sideOpts">
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While dragging in the plot, restrict to:<br>
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<span><input type="radio" name="fixAng" onClick="fix_a(0)" id="freeA" checked>none </span>
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<span><input type="radio" name="fixAng" onClick="fix_a('phi')">constant phi </span>
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<span><input type="radio" name="fixAng" onClick="fix_a('psi')">constant psi </span>
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</div>
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<div class="sideOpts">Or enter values:<br>
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<span style="padding-right:1ex;"><span class="greek">&#x03D5;</span> =
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<input type="text" id="phi_V" style="width:4.5ex;"></span>
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<span><span class="greek">&#x03C8;</span> =
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<input type="text" id="psi_V" style="width:4.5ex;"></span>
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<span><input type="button" value="apply" onClick="setStruct()"></span>
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</div>
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<div class="sideOpts">
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Structure rotation changing one angle:<br>
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<button onClick="rotate('phi');return false;"><span class="greek">&#x03D5;</span> play/pause</button>
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<button onClick="rotate('psi');return false;"><span class="greek">&#x03C8;</span> play/pause</button>
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</div>
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<div class="sideOpts">
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<input type="checkbox" id="bumps">
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<span style="border-bottom:3px solid magenta;border-top:3px solid magenta;">Highlight</span> collisions or clashes <br>
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(steric hindrance) <div class="Estilo1">(does not work during rotation)</div>
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</div>
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<div id="ramaLegend" style="clear:both; padding-top:0.3em;">
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...This uses the wikiPageContents tag:
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<p>Legend for Ramachandran plot:
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<jmol>
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</p>
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<size>220</size>
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<ul>
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<color>#EEEEFF</color>
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<li><span class="line" style="border-style:solid;"></span> boundary of rather stable conformations (favoured) </li>
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<jmolApplet>
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<li><span class="line" style="border-style:dashed;"></span> boundary of moderately stable conformations (allowed) </li>
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<wikiPageContents>Menthol</wikiPageContents>
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<li><b><span class="greek">&alpha;</span></b> alpha helix (right-handed, the usual one)</li>
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</jmolApplet>
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<li><b>L<span class="greek">&alpha;</span></b> left-handed alpha helix (less common)</li>
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</jmol>
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<li><b>3<sub>10</sub></b> 3_10 helix</li>
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...end
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<li><b>&beta;</b> beta strand, beta sheet</li>
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<li><b>poly P</b> polyproline helix (also collagen)</li>
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</ul>
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</div>
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</td>
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</tr>
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</table>
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...This uses the uploadedFileContents tag:
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<p style="font-size:0.8em; color:gray;">
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<jmol>
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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]
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<size>220</size>
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</p>
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<color>#EEEEFF</color>
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<jmolApplet>
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<uploadedFileContents>Menthol.mol</uploadedFileContents>
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</jmolApplet>
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</jmol>
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...end

Current revision

Test the extension

...This uses the inlineContents tag:

Drag the structure with the mouse to rotate

...end

...This uses the wikiPageContents tag:

Drag the structure with the mouse to rotate

...end

...This uses the uploadedFileContents tag:

Drag the structure with the mouse to rotate

...end

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez

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