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'''Templates as a tool'''
'''Templates as a tool'''


Existing templates can be used in Proteopedia pages to call commonly used wiki-text or Jmol code. A good description of how to use them, with color templates, can be found [[DRuMS#The DRuMS Color Schemes|here]]. Additional templates can be made, and you find a list of existing templates under [https://proteopedia.org/wiki/index.php?title=Special%3AAllpages&from=Abstract&namespace=10 All Pages].


This page is meant to be a resource for finding and using templates.


<StructureSection load='' size='300' side='right' caption='Surface to test templates' scene='60/607777/Surf_test/1' pspeed='8'>


==Surface display==


==Surface fade templates and buttons==
===Surface toggles===
<Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' caption='Surface Fade Demo Display' scene='60/607777/Surf_test/1' pspeed='8' />


These 3 controls are inserted using templates:


===Template Versions Ready to Use Anywhere Easily===
{{Button Toggle Surface}} · {{Link Toggle Surface}} · {{Checkbox Toggle Surface}} 
 
:<small>''Note to Wiki admin's: for the checkboxes to work, you must add a function setupCheckboxShiftClick() that overrides the one included in wikibits.js''</small>
 
===Surface fade templates===
Ready to use anywhere easily:


{{Link FadeSurfaceBasic}} (basic)
{{Link FadeSurfaceBasic}} (basic)
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{{Link FadeInSurface}}  
{{Link FadeInSurface}}  


As Buttons:<br/>
As buttons:<br/>


{{Button FadeSurfaceBasic}} (basic)
{{Button FadeSurfaceBasic}} (basic)
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{{Button FadeInSurface}}
{{Button FadeInSurface}}
   
   
 
===Surface fade code-in-page versions===
 
 
===Surface Fade Code-in-Page Versions===


While not templates, carry out similar functions as the `Surface Fade` templates and may be useful for further development or as examples of using Jmol coding in Proteopedia pages.
While not templates, carry out similar functions as the `Surface Fade` templates and may be useful for further development or as examples of using Jmol coding in Proteopedia pages.
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==Atom rendering style==


==Label-handling templates==
These controls are not templates, but inserted directly as wiki extension tags:


{{Link Toggle LabelsOff}} (No-demo made yet.)
<jmol>
<jmolCheckbox>
  <scriptWhenChecked>spacefill on</scriptWhenChecked>
  <scriptWhenUnchecked>spacefill off</scriptWhenUnchecked>
  <text>spacefill on/off</text>
</jmolCheckbox>
</jmol>


==Color Handling Templates==
<jmol>
  <jmolRadioGroup>
    <item>
      <text>spacefill on</text>
      <script>spacefill on</script>
    </item>
    <item>
      <text>spacefill off</text>
      <script>spacefill off</script>
    </item>
  </jmolRadioGroup>
</jmol>


* See [[DRuMS#The DRuMS Color Schemes|DRuMS color template]].
==Label handling==


Proteopedia's ''Scene Authoring Tool'' implement much of the DRuMS color schemes, but not all.
{{Link Toggle LabelsOff}} (No-demo made yet.)
Several portions not implemented concern nucleotides.
{{Template:ColorKey Purines}}, {{Template:ColorKey Pyrimidines}},
<br>
{{Template:ColorKey Bases Nucleotides}},
<br>
{{Template:ColorKey Bases DNA}},
<br>
{{Template:ColorKey Bases RNA}}.
</big></blockquote>


The above colored terms were generated by including the following Template wikitext blocks:
==Color handling==
<pre>
{{Template:ColorKey Purines}}
{{Template:ColorKey Pyrimidines}}
{{Template:ColorKey Bases Nucleotides}}
{{Template:ColorKey Bases DNA}}
{{Template:ColorKey Bases RNA}}
</pre>
<applet load='Image:Kt7.pdb.gz' size='250' frame='true' align='right' scene='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1' />A template exists for a related button that can be incorporated into Proteopedia pages and behaves similar to green scene link; when the button is pressed it results in coloring of the nucleotides according to the bases {{ColorKey Bases Nucleotides}}. Example:
{{Button Toggle NucleicDrumsColorScheme}}
<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1'>Reset</scene>


* See [[DRuMS#The DRuMS Color Schemes|DRuMS color template]].


&nbsp;
* See [[Help:Coloring_text#Color_Scheme_Templates|Color Scheme Templates]].
&nbsp;
 
 
Similarly, for {{Template:ColorKey Purines}}/{{ColorKey Pyrimidines}}:<br>
{{Button Toggle PurinePyrimidineDrumsColorScheme}}
<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1'>Reset</scene>
 
&nbsp;
 
{{Button Toggle NucleicDrumsColorScheme}}
 
{{Button Toggle NucleicDrumsColorSchemeWcartoon}}
 
{{Button Toggle PurinePyrimidineDrumsColorScheme}}
 
These are based on the following mnemonics for A, C, G, T, & U:
<br><b><big>
<font color="#5050ff">Azure</font>,
<font color="#e00000">Crimson</font>,
<font color="#00c000">Green</font>,
<font color="#d0d000">Tweety Bird</font>,
<font color="#cc9900">Umber</font>.</big></b>
<blockquote><big>
 
{{ColorKey Bases RNA}}
 
{{ColorKey Bases DNA}}
 
{{ColorKey Bases Nucleotides}}
 
{ColorKey Purines Pyrimidines}}


{{ColorKey Purines}}
Additional examples not listed there:


{{ColorKey Pyrimidines}}
{{Button ColorLeucine}}  


{{Button ColorLeucine}}
{{Button ColorReceptorLeucine}} (No-demo made yet.)


{{Button ColorReceptorLeucine}}
{{Button HeteroCPKColorScheme}} (No-demo made yet.)


{{Button HeteroCPKColorScheme}}
{{User:Wayne Decatur/Template ColorKey Composition lcprotein|Template ColorKey Composition protein}} - `protein` darkened for light backgrounds


</StructureSection>




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* [[Proteopedia:Cookbook]]
* [[Proteopedia:Cookbook]]
* [[DRuMS#The DRuMS Color Schemes|DRuMS color templates]]
* [[DRuMS#The DRuMS Color Schemes|DRuMS color templates]]
* [[Help:Color_Keys]]
* [[Help:Coloring_text]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Wayne Decatur, Angel Herraez, Karsten Theis
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