Proteopedia:How to Make a Page: Difference between revisions
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#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. | #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'. | #[[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> | #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> | ||
::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. | ||
## | ##new pages contain the code for this already | ||
##example wikitext: <nowiki> | ##example wikitext: <nowiki><StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> ... </StructureSection> | ||
</nowiki> | </nowiki> | ||
#the | #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 | #use an initial scene (by setting "load=''" and inserting the scene in the "scene=" parameter) | ||
#have | #make sure all your scenes have captions | ||
#include an interwiki link to the PDB entry in the | #include an interwiki link to the PDB entry in the captions | ||
#preferably | #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) | ||
==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 | ||