Proteopedia:DIY:Templates: Difference between revisions

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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)
Line 19: Line 28:
{{Link FadeInSurface}}  
{{Link FadeInSurface}}  


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


{{Button FadeSurfaceBasic}} (basic)
{{Button FadeSurfaceBasic}} (basic)
Line 27: Line 36:
{{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.
Line 59: Line 65:




==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>




Line 143: Line 117:
* [[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]]

Latest revision as of 16:20, 16 February 2021

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 here. Additional templates can be made, and you find a list of existing templates under All Pages.

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


Surface display

Surface toggles

These 3 controls are inserted using templates:

· ·

Note to Wiki admin's: for the checkboxes to work, you must add a function setupCheckboxShiftClick() that overrides the one included in wikibits.js

Surface fade templates

Ready to use anywhere easily:

(basic)

(with fancy cartoons)

As buttons:

(basic)

(with fancy cartoons)

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.

(basic)

(with fancy cartoons)


Atom rendering style

These controls are not templates, but inserted directly as wiki extension tags:

Label handling

(No-demo made yet.)

Color handling

Additional examples not listed there:

(No-demo made yet.)

(No-demo made yet.)

protein - `protein` darkened for light backgrounds


Surface to test templates

Drag the structure with the mouse to rotate


See AlsoSee Also

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

Jaime Prilusky, Wayne Decatur, Angel Herraez, Karsten Theis
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Proteopedia:DIY:Templates&oldid=3355039"