Proteopedia:How to Make a Page: Difference between revisions
Eran Hodis (talk | contribs) |
Undo revision 4304985 by Pooja Rajak (Talk) Tag: Manual revert |
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## the search box | ## the search box | ||
## looking in the [[Proteopedia:Table of Contents|table of contents]] | ## looking in the [[Proteopedia:Table of Contents|table of contents]] | ||
# choose a title that is appropriate | # choose a title that is appropriate following rules at [[Proteopedia:Page name]]. You can always rename the page later if necessary. | ||
#if a page on your topic already exists, you may edit that page to improve it | |||
# you don't have permission to edit [[1h88|PDB entry pages]]. Please contact {{Template:Contact}} if you need | |||
# don't edit | |||
## to add links to other Proteopedia pages | ## to add links to other Proteopedia pages | ||
## to correct wrong information about the PDB entry | ## to correct wrong information about the PDB entry | ||
## to add information relevant to the PDB entry but not to the protein or molecule in general | ## to add information relevant to the PDB entry but not to the protein or molecule in general | ||
#if a page on | #if you need to create a new page, search for the exact title of the new page, then in the "not found" results, click on the <font color='red'>red link</font> to the non-existent page. Now you can edit it, and after the first save, you have created the page. | ||
==The new page template== | |||
[[Image:Proteopedia New Page Annotated.JPG|right|thumb|New page template with highlighted code: 3D Jmol window, yellow; green links, green; references, tan.]]When you start a new page, it opens with a template to get you started. The elements highlighted in yellow place a 3D Jmol browser window on the right side of the page, with scrolling text on the left. The initial scene that shows in the 3D window is specified in the code as well, either by providing the PDB ID of a structure (here: 1STP) or by specifying a 3D scene (left blank in this example). The elements highlighted in green are the code that create green links on your page. The elements in tan show how to cite literature and show the references at the end of the page. You should modify these elements to fit your page. You could also delete the entire template and start from scratch if that is easier. | |||
==The basic beginnings of your page== | ==The basic beginnings of your page== | ||
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===Add a 2D image=== | ===Add a 2D image=== | ||
#preferably that show a different view of the protein compared to the 3D structure in the introduction, (i.e. if the introductory 3D structure is in cartoon, make the 2D image in spacefill) | #preferably that show a different view of the protein compared to the 3D structure in the introduction, (i.e. if the introductory 3D structure is in cartoon, make the 2D image in spacefill) | ||
#PyMOL is good for producing high-quality raytraced images for this purpose | #PyMOL is good for producing high-quality raytraced images for this purpose and you can use the [http://polyview.cchmc.org/polyview3d.html POLYVIEW-3D] webserver as a facile interface to rendering images with PyMol. Save the file to your computer. | ||
# | #[[Special:Upload|Upload]] the image file to Proteopedia using the '[[Special:Upload|Upload File]]' function under the toolbox section in the lower left hand side panel of each Proteopedia page. It will get a name such as 'Image:YourImageName.png'. | ||
#Build a reference to the uploaded image into your page. Example syntax: <nowiki>[[Image:YourImageName|300px|left|thumb| Your Caption Text]]</nowiki>::Example syntax if your image is derived from a PDB entry: <nowiki>[[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]</nowiki> | |||
#around 200 or 300 px is a good size | #around 200 or 300 px is a good size | ||
#the custom is to align the 2D image to the left | #the custom is to align the 2D image to the left | ||
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===Add a 3D structure=== | ===Add a 3D structure=== | ||
#standard practice is to use a | #standard practice is to use a "StructureSection", i.e. a window on the right with scrollable text on the left. | ||
##example wikitext: <nowiki> | ##new pages contain the code for this already | ||
##example wikitext: <nowiki><StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> ... </StructureSection> | |||
</nowiki> | </nowiki> | ||
#if | #if your page lacks a StructureSection and you need one, click on the "green window" icon in the editing tools | ||
#use an initial scene (by setting "load=''" and inserting the scene in the "scene=" parameter) | |||
#use an initial scene (by | #make sure all your scenes have captions | ||
#have | #include an interwiki link to the PDB entry in the captions | ||
#include an interwiki link to the PDB entry in the | #preferably show a different view of the protein compared to the 2D structure in the introduction, (i.e. if the introductory 2D image is in cartoon, make the 3D structure in spacefill) | ||
#preferably | |||
==Planning the rest of the page== | ==Planning the rest of the page== | ||
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# think about bringing the reader through a tour of the most interesting and important features of your structure | # think about bringing the reader through a tour of the most interesting and important features of your structure | ||
# plan for 1 or 2 sections that will feature a structural description with a 3D structure and green scene links | # plan for 1 or 2 sections that will feature a structural description with a 3D structure and green scene links | ||
# | # in exceptional cases, you might have more than one 3D applet on the page but this makes loading slower | ||
# plan for a section about how your topic is related to disease, if relevant | # plan for a section about how your topic is related to disease, if relevant | ||
==Rules to keep in mind== | ==Rules to keep in mind== | ||
* max number of applets on the entire page is 3 (use StructureSections to help reduce the number of applets on the page) | * max number of applets on the entire page is 3 (use StructureSections to help reduce the number of applets on the page, follow the examples here: [[Glutamate receptor (GluA2)|Glutamate receptor]]) | ||
* use wikitext rather than HTML | * use wikitext rather than HTML | ||
* mention all PDB ids whenever appropriate, and link to their page in Proteopedia | * mention all PDB ids whenever appropriate, and link to their page in Proteopedia | ||
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==Images== | ==Images== | ||
# images should ideally be big enough to look at without having to click to enlarge | # images should ideally be big enough to look at without having to click to enlarge | ||
# try to use this style of wikitext for images <nowiki>[[Image: | # [[Special:Upload|Upload]] the image file to Proteopedia using the '[[Special:Upload|Upload File]]' function under the toolbox section in the lower left hand side panel of each Proteopedia page. It will get a name such as 'Image:YourImageName.png'.Upload your image using the toolbox on the left | ||
# try to use this style of wikitext for images <nowiki>[[Image:YourImageName|300px|left|thumb| An informative caption here]]</nowiki> | |||
## change the caption, size and alignment (left, right, center) as necessary | ## change the caption, size and alignment (left, right, center) as necessary | ||
# provide a descriptive caption | # provide a descriptive caption | ||
# if the image is of a PDB entry, provide an interwiki link to that PDB entry in the caption | # if the image is of a PDB entry, provide an interwiki link to that PDB entry in the caption, for example <nowiki>[[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]</nowiki> | ||
# images should have proper copyrights that allow for their use in Proteopedia (do not use images from copyrighted sources like journal articles or textbooks) | # images should have proper copyrights that allow for their use in Proteopedia (do not use images from copyrighted sources like journal articles or textbooks) | ||
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##example wikitext: <nowiki><ref>PMID:1234235</ref></nowiki> | ##example wikitext: <nowiki><ref>PMID:1234235</ref></nowiki> | ||
#create a section titled "References" as the second to last section on the page (the last will be "External Resources") | #create a section titled "References" as the second to last section on the page (the last will be "External Resources") | ||
#in the "References" section add this wikitext: <nowiki><references/><nowiki> | #in the "References" section add this wikitext: <nowiki><references/></nowiki> | ||
#for more information on how to use references, refer to [[Help:Editing#Citing_Literature_References]] | #for more information on how to use references, refer to [[Help:Editing#Citing_Literature_References]] | ||
#make sure you cite, at the minimum, the most important references | #make sure you cite, at the minimum, the most important references | ||
==Add Internal Links== | ==Add Internal Links== | ||
# if there are topics mentioned in your page that have their own Proteopedia article, make them into interwiki links | # do a google search on your topic prepending it with "site:proteopedia.org" to discover which other pages are relevant to your topic.# if there are topics mentioned in your page that have their own Proteopedia article, make them into interwiki links | ||
## example wikitext: <nowiki>[[Hemoglobin]]</nowiki> | ## example wikitext: <nowiki>[[Hemoglobin]]</nowiki> | ||
# add a "See Also" section directly before the "References" section with a list of links to other Proteopedia pages (use the wikitext syntax for lists) | # add a "See Also" section directly before the "References" section with a list of links to other Proteopedia pages (use the wikitext syntax for lists) | ||
# consider editing the pages you linked to, adding a link to the new page. This way, Proteopedia becomes a web of linked pages, and it becomes easier to navigate. You can quickly find out about links from the "What links here" item in the toolbox on the left side panel. | |||
==List of all related PDB ids== | ==List of all related PDB ids== | ||
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# add categories to the bottom of your page | # add categories to the bottom of your page | ||
# if page topic fits within one of the subcategories listed in the table of contents, i.e. "Diabetes" or "Lyase" add a section at bottom of page, before the references section called "Additional Resources" with the phrase <nowiki>"See [[Diabetes]] for more information"</nowiki>. | # if page topic fits within one of the subcategories listed in the table of contents, i.e. "Diabetes" or "Lyase" add a section at bottom of page, before the references section called "Additional Resources" with the phrase <nowiki>"See [[Diabetes]] for more information"</nowiki>. | ||
==See Also== | |||
* [[Help:Editing]] | |||