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User:Wayne Decatur/Biochem642 Molecular Visualization Sessions: Difference between revisions

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Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,596 edits
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,596 edits
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**Click on 'edit this page' up at the top of the page.
**Click on 'edit this page' up at the top of the page.
**'''NOTE THE LAYOUT OF YOUR SANDBOX PAGE EDITING PAGE AND HOW IT IS CONTROLLING WHAT YOU SEE ON THE PAGE''':
**'''NOTE THE LAYOUT OF YOUR SANDBOX PAGE EDITING PAGE AND HOW IT IS CONTROLLING WHAT YOU SEE ON THE PAGE''':
***First is a line that is template telling others about your reservation and instructions not to delete.
***First is a line that is the template telling others about your reservation and instructions not to delete. (LEAVE THIS ALONE IN ALL EDITING YOU DO.)
***Next is the text of the title you saw which is in between some equal signs that just signals in wiki-talk, called wikitext, how that text is to be formatted special.
***Next is the text of the title you saw which is in between some equal signs that just signals in wiki-talk, called wikitext, how that text is to be formatted special.
***Next is wikitext beginning with '<applet' and ending by being closed with '/>'. All the text between '<applet' and '>/' just specifies the parameters of how to set up and what to show in the Jmol applet window where you saw the 1d66 structure spinning.
***Next is wikitext beginning with '<applet' and ending by being closed with '/>'. All the text between '<applet' and '>/' just specifies the parameters of how to set up and what to show in the Jmol applet window where you saw the 1d66 structure spinning.
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**'''Congratulations, you just edited your first Proteopedia page!'''
**'''Congratulations, you just edited your first Proteopedia page!'''
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*'''Now author a scene to add to your Sandbox page''':
*'''Now author a scene (view) to add to your Sandbox page''':
**Once again, click on 'edit this page' up at the top of the page.
**Once again, click on 'edit this page' up at the top of the page.
**Below the edit window (where you worked to change the title) you will see a picture of a protein next to text that says Scene authoring tools. Click on 'show' next to this and the Scene authoring tools will pop open below.  
**Below the edit window (where you worked to change the title) you will see a picture of a protein next to text that says Scene authoring tools. Click on 'show' next to this and the Scene authoring tools will pop open below.  
**Click on the 'load molecule' tab and enter 1d66 into the top box. Press the 'load' button.
**Click on the 'load molecule' tab and enter 1d66 into the top box. Press the 'load' button.
**Once you see the 1d66 structure in the window to the right (it won't be spinning), use the 'selections','representations', 'color' tab to change the scene in some manner. It doesn't matter exactly how because you are just practicing to learn the interface for now.
**Once you see the 1d66 structure in the window to the right (it won't be spinning), use the 'selections','representations', 'color' tab to change the scene in some manner. It doesn't matter exactly how because you are just practicing to learn the interface for now.
**Once you have a new scene, click the 'save scene' tab and give the scene a name and description.  
**Once you have a new scene, click the 'save scene' tab and give the scene a name and description. Choose whether you want it to molecule to spin or not when it is displayed.
**When you are satisfied with your name and description, '''press 'save scene' '''and you will see text show up in the box labeled 'wikitext' below.
**When you are satisfied with your name and description, '''press 'save scene' '''and you will see text show up in the box labeled 'wikitext' below.
*Note that at the end of this block of text and flanked my nowiki tags to tell the page not to process it as normal wikitext is wikitext very similar to what we just saw above; '''however, there is a significant difference: the scene parameter has been added in front of the caption parameter'''. In between the single quotes is the name of a dummy scene; there is no real scene corresponding to this name.
**Highlight and copy the text at the bottom of that box (all text after the colon), and paste it below the other text up in the edit window.
**'''Now hide the Scene Authoring tools'''by pressing 'hide' next to the name (where you pressed 'show' earlier) and the 'Save page' button will again be active. Click the 'Save page' button.
**'''Congratulations, you just made your first scene!'''
**'''However, you need to press the green text (green link) on your page to see it.''' If you click on it while viewing the page, the scene in the Jmol window at the right should change to it.  
 
 


*Make a scene (view) and add it to your Sandbox page.
*Make a scene (view) and add it to your Sandbox page.
*Make that scene show in the 3D applet window when the page comes up:
*'''Make the scene you made show in the 3D Jmol applet window when the page comes up''':
**BEFORE YOU OPEN EDIT, read the process on the normal page which I left for you. This part will remain untouched, at least for now.
**BEFORE YOU OPEN EDIT, read the process on the normal page which I left for you. This part will remain untouched, at least for now.
**
**
*Note that at the end of this block of text and flanked my nowiki tags to tell the page not to process it as normal wikitext is wikitext very similar to what we just saw above; '''however, there is a significant difference: the scene parameter has been added in front of the caption parameter'''. In between the single quotes is the name of a dummy scene; there is no real scene corresponding to this name.
**Click 'EDIT THIS PAGE', and add a scene tag to the 3D applet window information by copying the sample one (that generates the text you read from the page when not in editing mode) and putting it in the real one above. The one you pasted isn't a real scene name though! You need to get your scene information there.
**Click 'EDIT THIS PAGE', and add a scene tag to the 3D applet window information by copying the sample one (that generates the text you read from the page when not in editing mode) and putting it in the real one above. The one you pasted isn't a real scene name though! You need to get your scene information there.
**So copy the name of your scene between the single quotes down lower on the page, and replace the dummy text between the single quotes of the scene tag you just added to the 3D applet window information.
**So copy the name of your scene between the single quotes down lower on the page, and replace the dummy text between the single quotes of the scene tag you just added to the 3D applet window information.
*Load that same scene again in the Scene Authoring Tools using the load scene tab, modify it, and save a new scene. Paste the scene into your page.
*Load that same scene again in the Scene Authoring Tools using the load scene tab, modify it, and save a new scene. Paste the scene into your page.
*Add this scene as a new 3D window on the same page:
*Add this scene as a new 3D Jmol applet window on the same page:
**Copy the original applet
**Copy the original applet
*[[Help:Copying FirstGlance Scenes into Proteopedia|Copying FirstGlance Scenes into Proteopedia]]
*[[Help:Copying FirstGlance Scenes into Proteopedia|Copying FirstGlance Scenes into Proteopedia]]
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