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User:Jaime Prilusky/Test/Viewer: Difference between revisions

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ConfirmAccount, Editor, Journal, Mutation, Next, Print3D, Tester, any2jmol, Bureaucrats, Administrators
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Jaime Prilusky (talk | contribs)
ConfirmAccount, Editor, Journal, Mutation, Next, Print3D, Tester, any2jmol, Bureaucrats, Administrators
7,873 edits
No edit summary
 
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==Your Heading Here (maybe something like 'Structure')==
<SX load='1stp' size='400' side='right' viewer='molstar' caption='Caption for this structure' >__NOTOC__
<StructureSection load='' size='400' side='right' caption='Caption for this structure' scene='79/790359/Tst/2'>
==Selection of viewer engine==
This is a default text for your page '''Jaime Prilusky/Test/Cavity'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
The addition of the ''viewer'' parameter to ''&lt;StructureSection'' allows to choose between alternative engines for rendering a structure. Current valid values are '''jmol''' <ref>Jmol: an open-source browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D [http://jmol.org] </ref> (default) and '''molstar''' <ref>Mol* (/'molstar/) is an open collaboration started by PDBe and RCSB PDB to provide a technology stack for data delivery and analysis tools of macromolecules [https://molstar.org/]</ref>.  
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
==Under development==
A few features need additional development to work under different viewers, like &lt;scene>, initialView and SAT. Examples are these links to <scene name="/12/3456/Sample/1">color</scene> by Group, and to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein.
==Help on the tools==
The cheatsheet for using LiteMol viewer, available at [[http://www.ebi.ac.uk/pdbe/litemol PDBe]], should be Ok for the MolStar viewer in use.
==Scrolling page==
Alice was beginning to get very tired of sitting by her sister on the bank, and of having nothing to do: once or twice she had peeped into the book her sister was reading, but it had no pictures or conversations in it, ‘and what is the use of a book,’ thought Alice ‘without pictures or conversations?’


== Function ==
So she was considering in her own mind (as well as she could, for the hot day made her feel very sleepy and stupid), whether the pleasure of making a daisy-chain would be worth the trouble of getting up and picking the daisies, when suddenly a White Rabbit with pink eyes ran close by her.


There was nothing so very remarkable in that; nor did Alice think it so very much out of the way to hear the Rabbit say to itself, `Oh dear! Oh dear! I shall be late!' (when she thought it over afterwards, it occurred to her that she ought to have wondered at this, but at the time it all seemed quite natural); but when the Rabbit actually took a watch out of its waistcoat-pocket, and looked at it, and then hurried on, Alice started to her feet, for it flashed across her mind that she had never before seen a rabbit with either a waistcoat-pocket, or a watch to take out of it, and burning with curiosity, she ran across the field after it, and fortunately was just in time to see it pop down a large rabbit-hole under the hedge. <ref>Down the Rabbit-Hole. Alice's Adventures in Wonderland, by Lewis Carroll</ref>.


 
</SX>
<!-- The content below was inserted by the ConSurf template -->
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|right|200px]]
Check
<jmol>
  <jmolCheckbox>
<scriptWhenChecked>
select protein; define ~consurf_to_do selected;
consurf_initial_scene = true;
script /wiki/ConSurf/ea/1ea5_consurf.spt;
</scriptWhenChecked>
<scriptWhenUnchecked>
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB].
You may read the [[Conservation%2C_Evolutionary|explanation]]
of the method and the full data available from
[http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ea5 ConSurf].
<!-- end of content inserted by the ConSurf template -->
 
== Disease ==
 
== Relevance ==
 
== Structural highlights ==
 
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
 
</StructureSection>
== References ==
<references/>
<references/>
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