User:Eric Martz/Sandbox 5: Difference between revisions

Latest revision as of 21:58, 13 September 2023

Caption Rules

These rules are concluded from the tests below.

Your Heading Here (maybe something like 'Structure')

Anything in this section will appear adjacent to the 3D structure and will be scrollable.

Coloring Caption TextColoring Caption Text

Caption text can be colored using HTML:

Oxygen. displays Oxygen.

Colored text is easier to see in boldface. You can use either HTML or wikitext bold markup:

HTML: Oxygen. displays Oxygen.
Three single quotes: '''Oxygen'''. displays: Oxygen.

Light colors may be unreadable on a white background, so use a black background. But there seems to be no way to specify a background color in a caption. So you will need to put the color key in the text of the page. For standard color keys, templates are provided: see Help:Color Keys. Proteopedia page text does not support HTML bgcolor, but it supports CSS font color:

Yellow on white: Sulfur. displays yellow.
Yellow on black: Sulfur. displays Sulfur.

Links to Proteopedia PagesLinks to Proteopedia Pages

Links to Proteopedia pages, such as 6zgi (in wikitext, [[6zgi]], are NOT supported in captions. Put those links in the page text.

Caption TestsCaption Tests

Scene 1.

SCENE OK. CAPTION BAD FORMAT.
{{font color|#ef7000|426 pockets and cavities}} in 6zgi generated with the command <tt>isosurface cavity</tt>.
Proteopedia does not support this wikitext color method.

Scene 2.

NO SCENE, NO CAPTION.
426 pockets and cavities in [[6zgi]] generated with the command <tt>isosurface cavity</tt>.

Scene 4.

SCENE OK. CAPTION COLORED BUT NO 6zgi LINK.
426 pockets and cavities in [[6zgi]] generated with the command <tt>isosurface cavity</tt>.

Scene 5. .

NO SCENE. NO CAPTION.
Here is yellow text on a black background as a test.

Scene 6. .

NO SCENE. NO CAPTION.
Here is yellow text on a black background as a test.

Scene 7. .

NO SCENE. NO CAPTION.
Here is yellow text on a black background as a test.

Scene 8. .

NO SCENE. NO CAPTION.
Here is yellow text on a black background as a test.

</StructureSection>

@@ Line 1: / Line 1: @@
-__NOEDITSECTION__
+<StructureSection load='' size='350' side='right' caption='' scene=''>
-<big>Welcome to Proteopedia,</big>
+==Caption Rules==
+These rules are concluded from the tests below.
-<!--
+==Your Heading Here (maybe something like 'Structure')==
-The line below this paragraph, containing "STRUCTURE_1eve", creates the "Structure Box" on the page.
+<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1eve |  PDB= 1eve  |  SCENE=Main_Page/E2020_in_ache_spinning/1 }}
-The collaborative, 3D encyclopedia of proteins and other molecules.
-===<span style="color:green">Green</span> links change the 3D image!===
-<big>''Here's an excerpt from one of our pages ([[1eve]]):''</big>
-The anti-Alzheimer's drug E2020 (marketed as Aricept&reg;) is an inhibitor that binds acetylcholinesterase (AChE) with high affinity.  The X-ray structure of the E2020-AChE (AChE from ''Torpedo california'') complex shows that E2020 has a '''<scene name='1eve/E2020_close_up_with_84_279/12'>unique orientation</scene>''' along the active-site gorge, extending from the anionic subsite ('''<scene name='1eve/E2020_close_up_with_84lbld/6'>W84</scene>''') of the active site, at the bottom, to the peripheral anionic site ('''<scene name='1eve/E2020_close_up_with_84_279lbld/4'>near W279</scene>'''), at the top, via aromatic stacking interactions with conserved aromatic acid residues. E2020 does not, however, interact directly with either the catalytic triad or the 'oxyanion hole' but only '''<scene name='1eve/E20_interactionshown/7'>indirectly via solvent molecules</scene>'''.
+Anything in this section will appear adjacent to the 3D structure and will be scrollable.
-----
-===See more!===
+</StructureSection>
-<big>The [[Proteopedia:Video_Guide | Proteopedia Video Guide]] is a narrated video guide that serves both as a starting point as well as a reference.  </big>
-[[Image:Ipodtouch_hero_20080205.png|left|100px]]
+===Coloring Caption Text===
-===Page of the Year Competition===
-We're giving away a top-of-the-line [http://www.apple.com/ipodtouch/ 32Gb iPod touch] (generously donated by [http://www.idigital.co.il iDigital], [http://www.apple.com Apple's] representatives in Israel) to the winner of Proteopedia's Page of the Year Competition!  To learn more and to enter, visit [[Proteopedia:Page of the Year Competition]].
-{{Clear}}
-====Favorites====
+Caption text can be <font color="red">colored</font> using HTML:
-Here are several of our favorite pages. Visit them to get a feeling for Proteopedia:
+*<nowiki><font color="red">Oxygen</font>.</nowiki> displays <font color="red">Oxygen</font>.
-<table border="0"><tr><td>
-* [[Hemoglobin]]
-* [[HIV-1 protease]]
-* [[1eve | Acetylcholinesterase with the anti-Alzheimer's drug Aricept bound]]
-* [[Photosystem II]]
-* [[DNA]]
-</td><td>
-&nbsp; &nbsp;
-</td><td>
-* [[1v04 | Serum Paraoxonase-1 created by directed evolution]].
-* [[Recoverin, a calcium-activated myristoyl switch]] with [[Morphs|morphs]] of a dramatic conformational change.
-* [[1ogs | Human acid-beta-glucosidase]]
-* See also: [[Personal_favorites | Personal favorites pages]]
-</td></tr></table>
-====Browse!====
+Colored text is easier to see in boldface. You can use either HTML or wikitext bold markup:
-<table border="0"><tr><td>
+*HTML: <nowiki><font color="red"><b>Oxygen</b></font>.</nowiki> displays <font color="red"><b>Oxygen</b></font>.
-* [[Proteopedia:Interesting_Pages | Topic pages]]
+*Three single quotes: <nowiki><font color="red">'''Oxygen'''</font>.</nowiki> displays: <font color="red">'''Oxygen'''</font>.
-* [[Personal_favorites | Personal favorites]]
-* [[Highest_impact_structures | Highest impact structures of all time]]
-* [[About Macromolecular Structure]]
-</td><td>
-&nbsp; &nbsp;
-</td><td>
-* [[Special:Popularpages | Most-popular pages]]
-* [[Special:Mostrevisions | Most-revised pages]]
-* [[Special:Longpages | Longest pages]]
-* [[Special:Recentchanges | Most-recent changes]]
-</td><td>
-&nbsp; &nbsp;
-</td><td>
-* [[Special:Newpages | Newest pages]]
-* [[Special:Random | Random page]]
-* [[Special:Listusers | User list]]
-* [[Believe_It_or_Not%21 | Believe It or Not!]]
-</td><td>
-&nbsp; &nbsp;
-</td><td>
-* [[Proteopedia:News|News]]
-* [[Special:Statistics | Statistics]]
-</td></tr></table>
-----
-===How can I find my protein/molecule?===
+Light colors may be unreadable on a white background, so use a black background. But there seems to be '''no way to specify a background color in a caption'''. So you will need to put the color key in the text of the page. For standard color keys, templates are provided: see [[Help:Color Keys]]. Proteopedia page text does not support HTML bgcolor, but it supports CSS font color:
-<big>'''Search'''</big> Proteopedia using the search box in the toolbar to the left. See also [[Help:Searching]].
+*Yellow on white: <nowiki><font color="yellow"><b>Sulfur</b></font>.</nowiki> displays <font color="yellow"><b>yellow</b></font>.
-Proteopedia already contains '''>50,000 pages''', including an automatically-generated page for every published macromolecular 3D structure (to see some of these, click ''Random Page'' in the navigation box at the upper left), plus [[Proteopedia:Topic Pages | Topic Pages]] providing an overview of a class of molecules or other structural topics.
+<!--*Yellow on black: <nowiki><font color="yellow" bgcolor="black"><b>yellow</b></font>.</nowiki> displays <font color="yellow" bgcolor="black">Sulfur</font>.-->
+*Yellow on black: <nowiki><font style="background-color:black;color:yellow;padding: 3px 4px 2px 4px;">Sulfur</font>.</nowiki> displays <font style="background-color:black;color:yellow;padding: 3px 4px 2px 4px;">Sulfur</font>.
-===Want to contribute?===
+===Links to Proteopedia Pages===
+Links to Proteopedia pages, such as [[6zgi]] (in wikitext, <nowiki>[[6zgi]]</nowiki>, are NOT supported in captions. Put those links in the page text.
-<font color='green'>Green links</font> are easy to make! We encourage you to '''edit pages freely''' and to '''[[Help:Editing#How_To_Create_A_New_Page | add new pages]].
-You will need a user account in order to edit or add pages. Please go ahead and '''[[Special:RequestAccount|request a user account]]'''.
+==Caption Tests==
-If you have any questions, you can email {{Template:Contact}}.
+Scene 1. <scene name='32/324686/1/1'>Wikitext color* and boldface</scene>
+*SCENE OK. CAPTION BAD FORMAT.
+*<nowiki><b>{{font color|#ef7000|426 pockets and cavities}}</b> in 6zgi generated with the command <tt><b>isosurface cavity</b></tt>.</nowiki>
+*Proteopedia does not support this wikitext color method.
-These resources may help you familiarize yourself with the editing process.  Trust us, the editing process is very simple: All text is edited the same way that Wikipedia is edited, so it must be easy! And all scenes (green links) are created using our user-friendly ''Scene authoring tools''.  Of course it helps to familiarize yourself with the site and how to go about editing, so check out these resources:
+Scene 2. <scene name='32/324686/1/2'>HTML color, escaped double quotes, and 6zgi linked</scene>
-*<big>The [[Proteopedia:Video_Guide | Proteopedia Video Guide]] is a narrated video guide that serves both as a starting point as well as a reference.  </big>
+*NO SCENE, NO CAPTION.
-*The [[Help:Editing | '''Editing Help Page''']].
+*<nowiki><b><font color=\"#ef7000\">426 pockets and cavities</font></b> in [[6zgi]] generated with the command <tt><b>isosurface cavity</b></tt>.</nowiki>
-*The help page for the [[Scene authoring tools]].
-* [[Proteopedia:Policies]]
-===What Can Proteopedia Do For Me?===
+Scene 4. <scene name='32/324686/1/4'>HTML color, double quotes NOT escaped, and 6zgi linked</scene>
-* Scientists and Students: a reference resource for understanding protein 3D structure-function relationships. Example: [[1eve | Acetylcholinesterase bound to Aricept, an anti-Alzheimer's drug]].
+*SCENE OK. CAPTION COLORED BUT NO 6zgi LINK.
-* Educators: develop tutorials or molecular scenes to project during lectures, or for student use. Examples: [[Teaching Scenes, Tutorials, and Educators' Pages]]. Assign students to construct pages in Proteopedia for class projects or reports: see [[Student Projects]]. See also [[Teaching Strategies Using Proteopedia]].
+*<nowiki><b><font color="#ef7000">426 pockets and cavities</font></b> in [[6zgi]] generated with the command <tt><b>isosurface cavity</b></tt>.</nowiki>
-You may protect your teaching pages from unwanted editing by others -- see [[Help:Protected Pages]].
-* Structural Researchers: create supplementary materials for your journal publications, and pages about your research team or institute, highlighting structures you have researched. For examples, see [[Research Groups]].
-You may protect such pages from unwanted editing by others -- see [[Help:Protected Pages]].
-===Proteopedia Mission Statement===
+Scene 5. <scene name='32/324686/1/5'>CSS span style colors, double quotes</scene>.
-To collect, organize and disseminate structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists.
+*NO SCENE. NO CAPTION.
+*<nowiki>Here is <span style="color:yellow;background-color:black;">yellow text on a black background</span> as a test.</nowiki>
-===Goals for Proteopedia===
+Scene 6. <scene name='32/324686/1/6'>CSS font style colors, double quotes</scene>.
-* To serve as a forum for the scientific community to share, retrieve and discuss information related to proteins, macromolecules, and small molecules and chemicals of interest.
+* NO SCENE. NO CAPTION.
-* To continue to develop the concept of tying text to three-dimensional, interactive images.
+*<nowiki>Here is <font style="color:yellow;background-color:black;">yellow text on a black background</font> as a test.</nowiki>
-* To maintain low barriers for contribution.
-* To foster collaborations between students and experts, signed with their real names.
-===About Proteopedia: How to Cite Proteopedia / News/ Contact ===
+Scene 7. <scene name='32/324686/1/7'>CSS font style colors, single quotes</scene>.
-On the page '''[[Proteopedia:About | About Proteopedia]]''' you will find information about how to cite Proteopedia, and its contents, implementation, policies and credits. At '''[[Proteopedia: News]]''' you will find current events concerning Proteopedia, such as press reports, blogs, meeting reports and seminars, training workshops, and a list of databases and structural bioinformatics resources that offer links to Proteopedia.
+* NO SCENE. NO CAPTION.
+*<nowiki>Here is <font style='color:yellow;background-color:black;'>yellow text on a black background</font> as a test.</nowiki>
-If you have any questions, please contact {{Template:Contact}}.
+Scene 8. <scene name='32/324686/1/8'>CSS font style colors, '''escaped''' single quotes</scene>.
+* NO SCENE. NO CAPTION.
+*<nowiki>Here is <font style=\'color:yellow;background-color:black;\'>yellow text on a black background</font> as a test.</nowiki>
-===Mugs and T-Shirts===
-<gallery widths="150px" align="left">
+</StructureSection>
-Image:Proteopedia_mug.jpeg
-Image:Proteopedia_T-shirt.jpeg
-</gallery>
-Proudly show your love for Proteopedia and help spread Proteopedia's wonders with highly coveted mugs and T-shirts from [http://www.cafepress.com/molviz4 cafepress.com], featuring the original Proteopedia logo by Tali Wiesel. Cafepress is a website that prints custom images on mugs and T-shirts, and is unaffiliated with Proteopedia. Proteopedia collects no money from your purchase.
-{{Clear}}