Remixing: Difference between revisions
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=== Finding the scene block === | === Finding the scene block === | ||
Let's say you want to reuse a 3D scene you found on an existing Proteopedia page. To remix the 3D scene, you need the scene block for the scene, that looks like this <span style='background-color:#cecece;'><scene name='77/778334/A_chain/1'>green link text</scene></span>. Go into the edit tab of the source page and look for the 'scene' tags. | Let's say you want to reuse a 3D scene you found on an existing Proteopedia page. To remix the 3D scene, you need the scene block for the scene, that looks like this <span style='background-color:#cecece;'><scene name='77/778334/A_chain/1'>green link text</scene></span>. Go into the edit tab of the source page and look for the 'scene' tags. Once you have copied the information, cancel the edit of the existing Proteopedia page. | ||
=== Using the scene as is === | === Using the scene as is === | ||
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=== Modifying scenes called through a Jmol link === | === Modifying scenes called through a Jmol link === | ||
This section is an advanced topic, and only applies to pages that use jmolLink blocks. Some green links don't have a scene block but rather have a jmolLink block, e.g. | This section is an advanced topic, and only applies to pages that use jmolLink blocks. Some green links on a few pages don't have a scene block but rather have a jmolLink block, e.g. | ||
<jmol><jmolLink> | <jmol><jmolLink> | ||
<script> | <script> | ||
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This example is from [[Hen Egg-White (HEW) Lysozyme]]. | This example is from [[Hen Egg-White (HEW) Lysozyme]]. | ||
If there is a call to a script like in this example, you can copy the entire block (from <jmol > to </jmol >) and paste it into the new page. Once it is saved in your new page, the scene will be accessible in the scene authoring tools. However, it will lack any additional commands from the <script > block (e.g. the ones in the example highlighting hydrogen bonds in the sheets). | If there is a call to a script like in this example, you can copy the entire block (from <jmol > to </jmol >) and paste it into the new page. Once it is saved in your new page, the scene ("37/376372/Hbonds/2") will be accessible in the scene authoring tools. However, it will lack any additional commands from the <script > block (e.g. the ones in the example highlighting hydrogen bonds in the sheets). | ||
== Remixing scenes from Proteopedia as images == | == Remixing scenes from Proteopedia as images == | ||
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The quickest way to save a 2D image from a 3D scene is to take a screenshot, but it is not the best. To get more control over image size, and to capture the information necessary to go back to a 3D scene, open the Jmol console to issue this command: | The quickest way to save a 2D image from a 3D scene is to take a screenshot, but it is not the best. To get more control over image size, and to capture the information necessary to go back to a 3D scene, open the Jmol console to issue this command: | ||
<pre>write IMAGE width height PNGJ n "fileName"</pre> | <pre>write IMAGE width height PNGJ n "fileName"</pre> | ||
In this command, "width" and "height" are the size of the image in pixels, and "n" is an integer between 0 and 10 indicating the degree of compression to reduce the file size. The filename should have a .png extension to indicate the image format. | In this command, "width" and "height" are the size of the image in pixels, and "n" is an optional integer between 0 and 10 indicating the degree of compression to reduce the file size. The filename should have a .png extension to indicate the image format. | ||
If you want a 3D effect, saving as an animated GIF works for many types of media (slides, web pages). In Proteopedia, the 3D Jmol windows have an animation link on the bottom. Click on this and follow instructions to make a rotating or rocking animated GIF from the 3D scene. The following animated GIF was made from the alpha helix scene shown below. To learn about the parameters used, click on the image. | If you want a 3D effect, saving as an animated GIF works for many types of media (slides, web pages). In Proteopedia, the 3D Jmol windows have an animation link on the bottom. Click on this and follow instructions to make a rotating or rocking animated GIF from the 3D scene. The following animated GIF was made from the alpha helix scene shown below. To learn about the parameters used, click on the image. | ||
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<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''> | <StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''> | ||
# Here is the <scene name='86/860406/Hairpin_morph/1'>beta hairpin folding morph</scene>. The original is in a Jmol window on | # Here is the <scene name='86/860406/Hairpin_morph/1'>beta hairpin folding morph</scene>. The original is in a Jmol window on an external web page (ChemTube3D, see attribution at end of article). The coordinates were uploaded to Proteopedia ([[Image:Hairpin3anim.pdb]]), and the state file used in the original was run on these coordinates to create the scene in the scene authoring tool of Proteopedia. | ||
# Here is the <scene name='86/860406/1hhb_helix/1'>alpha helix</scene>. This is directly used from the [[alpha helix]] page. | # Here is the <scene name='86/860406/1hhb_helix/1'>alpha helix</scene>. This is directly used from the [[alpha helix]] page. | ||
# And here we go to <scene name='86/860406/Complex/1'>1D66</scene>. Another example of a scene from the [[alpha helix]] page. | # And here we go to <scene name='86/860406/Complex/1'>1D66</scene>. Another example of a scene from the [[alpha helix]] page. | ||
</StructureSection> | </StructureSection> | ||
