User:Wayne Decatur/Biochem642 Sandbox Steps: Difference between revisions
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*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', and/or '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. Choose whether you want it to molecule to spin or not when it is displayed. | *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. | ||
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*Go ahead now and click on 'edit this page' up at the top of the page. | *Go ahead now and click on 'edit this page' up at the top of the page. | ||
*We will finally consider the last block of text in the edit window: | *We will finally consider the last block of text in the edit window: | ||
**Note that at the end of this block of text and flanked by nowiki tags to tell the page not to process it as normal wikitext is wikitext for a 3D Jmol applet window very similar to what we saw above; '''however, there is a significant difference: the scene parameter has been added in front of the caption parameter'''. | **Note that at the end of this block of text and flanked by nowiki tags to tell the page not to process it as normal wikitext is wikitext for a 3D Jmol structure applet window very similar to what we 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 for the scene parameter is the name of a dummy scene; there is no real scene corresponding to this name. | **In between the single quotes for the scene parameter is the name of a dummy scene; there is no real scene corresponding to this name. | ||
*In the edit window, the wikitext for the currently active Jmol applet window right now reads : <br> <nowiki>< | *In the edit window, the wikitext for the currently active Jmol applet window right now reads : <br> <nowiki><Structure load='1d66' size='300' frame='true' align='right' caption='Your caption here.' /></nowiki> | ||
*Add a scene parameter tag to the 3D applet window information wikitext by copying the text from the sample one and pasting it in the wikitext for the active one just in front of 'caption'. Note: the one you pasted isn't a real scene name though! It will now resemble:<br> <nowiki>< | *Add a scene parameter tag to the 3D applet window information wikitext by copying the text from the sample one and pasting it in the wikitext for the active one just in front of 'caption'. Note: the one you pasted isn't a real scene name though! It will now resemble:<br> <nowiki><Structure load='1d66' size='300' frame='true' align='right' caption='Your caption here.' scene='Sandbox/TestScene/1' /></nowiki> | ||
*You need to get your scene information in the Jmol window by changing the dummy name to the name of your scene: | *You need to get your scene information in the Jmol window by changing the dummy name to the name of your scene: | ||
**Copy the name of your scene from the wikitext you pasted before that made the green link. Just copy the name that is between the sing quotes. | **Copy the name of your scene from the wikitext you pasted before that made the green link. Just copy the name that is between the sing quotes. | ||
**Replace the dummy text between the single quotes of the name parameter of the wikitext for the Jmol applet window with your scenes name by now pasting it between those single quotes. It will now resemble:<br> <nowiki>< | **Replace the dummy text between the single quotes of the name parameter of the wikitext for the Jmol applet window with your scenes name by now pasting it between those single quotes. It will now resemble:<br> <nowiki><Structure load='1d66' size='400' frame='true' align='right' caption='Your caption here.' scene='SandboxNUMBER/YOURSceneHERE/1'/></nowiki> | ||
**Press 'Save the page' below. | **Press 'Save the page' below. | ||
*'''Your scene should now come up automatically when the page starts up!''' | *'''Your scene should now come up automatically when the page starts up!''' | ||
===Editing the caption below the Jmol applet window=== | ===Editing the caption below the Jmol applet window=== | ||
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===Showing | ===Showing additional scenes on your Sandbox page=== | ||
#Make another scene and save it. (You can keep the same name because it will get a new version number.) | #Make another scene and save it. (You can keep the same name because it will get a new version number.) | ||
#As you did before, copy and then paste the wikitext you need for that scene above in the edit window. | #As you did before, copy and then paste the wikitext you need for that scene above in the edit window. | ||
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#Edit the text between the single quotes of the scene parameter and the caption parameter to suit the new scene. | #Edit the text between the single quotes of the scene parameter and the caption parameter to suit the new scene. | ||
#Hide the Scene authoring tool, if you haven't done so yet, and save the page. You now should have two Jmol applet windows on your page. One with your old scene and one with your new one. | #Hide the Scene authoring tool, if you haven't done so yet, and save the page. You now should have two Jmol applet windows on your page. One with your old scene and one with your new one. | ||
===You have completed the basic editing and authoring steps=== | ===You have completed the basic editing and authoring steps=== | ||
*It is suggested you at least look at [[User:Wayne Decatur/Biochem642 Sandbox Steps#Items that may be useful|the items that may be useful]] below so that if you run into similar issues, you know where to find the answer. | *It is suggested you at least look at [[User:Wayne Decatur/Biochem642 Sandbox Steps#Items that may be useful|the items that may be useful]] below so that if you run into similar issues, you know where to find the answer. | ||
*When you do your problem sets and create new scenes, you can edit the Jmol windows you already have by changing the name of the scene in the wikitext specifying the window. You don't have to change the name in the 'load' paramaeter within the Jmol window wikitext because the scene will open with the right pdb file if it was used when making the scene. | |||
*Go back to the [[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions|Outline of the Sessions]] and examine the rest of the entries under [[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions#Authoring Scenes and Views in Proteopedia and beyond|Authoring Scenes and Views in Proteopedia and beyond]]. | *Go back to the [[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions|Outline of the Sessions]] and examine the rest of the entries under [[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions#Authoring Scenes and Views in Proteopedia and beyond|Authoring Scenes and Views in Proteopedia and beyond]]. | ||
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===Nicely arranging multiple Jmol applet windows=== | ===Nicely arranging multiple Jmol applet windows=== | ||
*Using 'left', 'right' and 'center' align tags with small window size allows easy arrangement: [[User:Wayne Decatur/Applet side by side demo| example page here]] | |||
*Tables also provide a simple way to control the arrangement of Jmol Applet windows on a Proteopedia page, for examples see [[User:Wayne Decatur/Sandbox Controlled Applet Layout| here]]. | |||
**Tables are specified by wikitext or html within the code controlling the page that you see when you go to 'edit this page'. | |||
***Using wikitext markup or html is your own choice. Both do the same; they just use different syntax for specifying columns and rows. | |||
***Some people may be more familiar with HTML or have HTML editors that they can use to facilitate these efforts. | |||
**To help I have made a page with some useful examples: | |||
***The page is: [[User:Wayne Decatur/Sandbox Controlled Applet Layout| here]] | |||
***You should be able to copy and paste the code of the examples and then adapt them to your scenes by pasting your code for 3D Jmol applet windows where I had sample wikitext for Jmol applet windows. | |||
***Remember, you copy always copy the code from any page and edit in a page to which you have access. | |||
===Getting wikitext or scene names for old scenes or if you forgot to copy the scene before:=== | ===Getting wikitext or scene names for old scenes or if you forgot to copy the scene before:=== | ||
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*If you want to explore further authoring or scripting, look at other Proteopedia pages and see the [[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions#Authoring Scenes and Views in Proteopedia and beyond|resources on the page for the work sessions]] too. | *If you want to explore further authoring or scripting, look at other Proteopedia pages and see the [[User:Wayne Decatur/Biochem642 Molecular Visualization Sessions#Authoring Scenes and Views in Proteopedia and beyond|resources on the page for the work sessions]] too. | ||
==Class Sandboxes== | |||
== | |||
{| | {| | ||
|width="225"| [[Sandbox | |width="225"| [[Sandbox Reserved 101]] | ||
|width="225"| [[Sandbox | |width="225"| [[Sandbox Reserved 111]] | ||
|width="225"| [[Sandbox | |width="225"| [[Sandbox Reserved 121]] | ||
|width="225"| [[Sandbox | |width="225"| [[Sandbox Reserved 131]] | ||
|width="225"| [[Sandbox Reserved 141]] | |||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 102]] || [[Sandbox Reserved 112]] || [[Sandbox Reserved 122]] || [[Sandbox Reserved 132]] ||[[Sandbox Reserved 142]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 103]] || [[Sandbox Reserved 113]] || [[Sandbox Reserved 123]] || [[Sandbox Reserved 133]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 104]] || [[Sandbox Reserved 114]] || [[Sandbox Reserved 124]] || [[Sandbox Reserved 134]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 105]] || [[Sandbox Reserved 115]] || [[Sandbox Reserved 125]] || [[Sandbox Reserved 135]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 106]] || [[Sandbox Reserved 116]] || [[Sandbox Reserved 126]] || [[Sandbox Reserved 136]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 107]] || [[Sandbox Reserved 117]] || [[Sandbox Reserved 127]] || [[Sandbox Reserved 137]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 108]] || [[Sandbox Reserved 118]] || [[Sandbox Reserved 128]] || [[Sandbox Reserved 138]] | ||
|- | |- | ||
| [[Sandbox | | [[Sandbox Reserved 109]] || [[Sandbox Reserved 119]] || [[Sandbox Reserved 129]] || [[Sandbox Reserved 139]] | ||
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| [[Sandbox | | [[Sandbox Reserved 110]] || [[Sandbox Reserved 120]] || [[Sandbox Reserved 130]] || [[Sandbox Reserved 140]] | ||
|} | |} | ||
