Forms of DNA: Difference between revisions

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Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
new source to fix failures with animated model
Angel Herraez (talk | contribs)
Editor, Macro, Print3D, Tester
1,212 edits
rewriting the source code for the aimated transition, to fix nonfunctioning part
Line 103: Line 103:
   <jmolButton>
   <jmolButton>
     <target>AtoB</target>
     <target>AtoB</target>
     <script>spacefill only;</script>
     <script>spacefill only; save state ab;</script>
     <text>Spacefill</text>
     <text>Spacefill</text>
   </jmolButton>
   </jmolButton>
</jmol>
</jmol>


</StructureSection>
<scene name='43/438459/Spacefill_animated/3'>Reset the model</scene>
 
 
<!--To activate the below options saving initial state again as restore state after above step is not working-->
<jmol>
<jmolButton>
<target>AtoB</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script> <!-- This is required as the initial save state is unable to restore state-->
<text>Click here and activate the below options </text>
</jmolButton>
</jmol>


<!--Group of Actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
<!--Group of actions which show base pair shift, sugar pucker change and difference in space filling models in A and B DNA -->
Other interesting views:
<jmol>
<jmol>
  <jmolRadioGroup>
<jmolRadioGroup>
<target>AtoB</target>
  <target>AtoB</target>
<item>
  <vertical>true</vertical>
    <script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab; animation mode palindrome;animation ON;cartoon ON;spacefill on; spacefill 90;wireframe on;wireframe 50;zoom 180;select 9:a,4:b;hbonds ON;hbonds calculate;hbonds 0.09;select not selected; color translucent 0.9;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo "Base pair shift between A and B DNA"</script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
   <item>
   <item>
   <script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;cartoon OFF;spacefill ON; spacefill 90; wireframe ON; wireframe 50;select 9:a; select not selected; color translucent 0.9; select not selected; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo "Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"; animation mode palindrome;animation ON;</script>
   <script>moveto 1 0 0 1 0 180 0 0; spin off; select all; cartoon only; spacefill 90; wireframe 50; centre all; zoom 180;  
    <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
color translucent 0.9; select 9:A,4:B; hbonds calculate; hbonds 0.09; color opaque;  
  </item>
set echo bottom centre; font echo 18 serif bold; color echo green; echo "Base pair shift between A and B DNA";
anim mode palindrome; anim on;</script>
  <text>Shift in base pair between A- and B- DNA</text>
  </item>
   <item>
   <item>
   <script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;spacefill ON; spacefill 400; zoom 150; cartoon OFF; animation mode PALINDROME;animation ON; set echo bottom centre;font echo 20 serif bolditalic;color echo green; echo"Transition between A-B DNA spacefilling models"; </script>
   <script>moveto 1 0 0 1 0 400 0 0; spin off; select all; spacefill only; spacefill 90; wireframe 50;
    <text>Transition between A-B DNA spacefilling models</text>
color translucent 0.9; select 9:A; color opaque; centre selected; zoom 400;  
  </item>
set echo bottom left; font echo 18 serif bold; color echo green; echo "Change in sugar puckering |from C2' endo in B-DNA to C3' endo in A-DNA";
  </jmolRadioGroup>
anim mode palindrome; anim on;</script>
  <text>Change in sugar puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  </item>
</jmolRadioGroup>
</jmol>
</jmol>


<!-- Restores Original State for Applet 4-->
<jmol>
<jmolButton>
<target>AtoB</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/9/9e/Morph_a-b.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Restore Original State </text>
</jmolButton>
</jmol>


Source of morphs: <ref>PMID: 10734184</ref>


<!-- Applet 5-->
[[Morphs|Read more about morphing]]
<!--<jmol>
  <jmolApplet>
    <color>white</color>
      <size>660</size>
    <uploadedFileContents>Morph_test.pdb</uploadedFileContents>
    <script>animation ON;animation mode PALINDROME;cartoon ON; save state ab_new</script>
  </jmolApplet>
</jmol>
 
<jmol>
<jmolButton>
<target>6</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Click here and activate options below </text>
</jmolButton>
</jmol>
 
<jmol>
  <jmolRadioGroup>
<target>6</target>
<item>
    <script> moveto 1.0 0 0 1 0 180.0 0.0 0.0;restore state ab;define temp selected; cartoon ON; spacefill 90; wireframe 50;zoom 180;select 9:a,4:b;hbonds calculate;hbonds 0.09; color translucent 0.9;set echo bottom centre;font echo 20 serif bold;color echo green; echo"Shift in Base Pair between A-B DNA"; select temp; animation mode palindrome;animation ON; </script>
<text>Shift in Base Pair between A-B DNA</text>
</item>
  <item>
  <script> moveto 1.0 0 0 1 0 400.0 0.0 0.0; restore state ab;define temp selected; cartoon OFF; spacefill 90; wireframe 50;select not 9:a; color translucent 0.9; centre selected;zoom 400;set echo bottom centre;font echo 20 serif bold;color echo green; echo"Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA"; select temp; refresh; animation mode palindrome;animation ON; </script>
    <text>Change in Sugar Puckering from C2' endo in B-DNA to C3' endo in A-DNA</text>
  </item>
  <item>
  <script>moveto 1.0 0 0 1 0 150.0 0.0 0.0;restore state ab;define temp selected; cartoon OFF;spacefill 400; zoom 150; set echo bottom centre;font echo 20 serif bold;color echo green; echo"Transition between A-B DNA spacefilling models"; select temp; animation mode palindrome;animation ON; </script>
    <text>Transition between A-B DNA spacefilling models</text>
  </item>
  </jmolRadioGroup>
</jmol>
 
<jmol>
<jmolButton>
<target>6</target>
<script>moveto 1.0 0 0 1 0 100.0 0.0 0.0;load/wiki/images/5/50/Morph_test.pdb;animation ON; animation mode PALINDROME; cartoon ON;save state ab</script>
<text>Restore Original State </text>
</jmolButton>
</jmol>-->
 
''Morph Sources'' <ref>PMID: 10734184</ref> / [[Morphs]]




Line 217: Line 160:
</jmol>-->
</jmol>-->


</StructureSection>
== References==
== References==
<references/>
<references/>
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