Proteopedia:DIY:Templates

From Proteopedia

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.

1 Surface display
2 Atom rendering style
3 Label handling
4 Color handling

Surface display

Surface toggles

These 3 controls are inserted using templates:

· Toggle Surface ·

show surface

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:

Fade surface to invisible (basic)

Fade surface to invisible (with fancy cartoons)

Fancy, high-quality cartoons on/off

Fade back to surface opaque

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.

Fade surface to invisible (basic)

Fade surface to invisible (with fancy cartoons)

Fade back to surface opaque

Atom rendering style

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

spacefill on/off

spacefill on spacefill off

Label handling

Turn off labels. (No-demo made yet.)

Color handling

See DRuMS color template.

See Color Scheme Templates.

Additional examples not listed there:

(No-demo made yet.)

protein - `protein` darkened for light backgrounds

loadScript /wiki/extensions/jsmol/j2s/core/package.js

loadScript /wiki/extensions/jsmol/j2s/core/corejmol.z.js

loadScript /wiki/extensions/jsmol/j2s/J/translation/PO.js

loadScript /wiki/extensions/jsmol/j2s/core/corescript.z.js

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__125854342345197__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__125854342345197__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://proteopedia.org/wiki/index.php/Proteopedia:DIY:Templates","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__125854342345197__","codePath":"https:/wiki/extensions/jsmol/j2s/","display":"jmolApplet1_canvas2d","loadStructCallback":"manageLoadStructCallback","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"125854342345197","messageCallback":"msgCb","bgcolor":"white" }

setting document base to "https://proteopedia.org/wiki/index.php/Proteopedia:DIY:Templates"

Jmol Version: 14.31.8 2020-09-26 10:04

java.vendor: Java2Script (HTML5)

java.version: 2019-06-08 00:17:46 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet1 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback manageLoadStructCallback

LOADSTRUCTCallback = "manageLoadStructCallback"

StatusManager callback set for LOADSTRUCTCallback f=manageLoadStructCallback cb=LOADSTRUCT

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback msgCb

MESSAGECallback = "msgCb"

StatusManager callback set for MESSAGECallback f=msgCb cb=MESSAGE

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue doTranslate null

Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet()

Note -- language translation disabled

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1__125854342345197__ ready

script 1 started

pdbGetHeader = true

FileManager opening url https://proteopedia.org/wiki/extensions/Proteopedia/spt/functions.spt?1733933141

loadScript /wiki/extensions/jsmol/j2s/core/coretext.z.js

Loading, please wait ...

Surface to test templates

Drag the structure with the mouse to rotate

Export Animated Image

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Karsten Theis, Angel Herraez, Jaime Prilusky

Retrieved from "http://proteopedia.org/wiki/index.php/Proteopedia:DIY:Templates"

Proteopedia:DIY:Templates

From Proteopedia

Contents

Surface display

Surface toggles

Surface fade templates

Surface fade code-in-page versions

Atom rendering style

Label handling

Color handling

See Also

Proteopedia Page Contributors and Editors (what is this?)

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