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

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 *[[Help:Editing|How to edit pages in Proteopedia]] → [[Ribosome|Example 1]], [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|example 2]], and [[Avian Influenza Neuraminidase, Tamiflu and Relenza|example 3]] of edited topic pages.
 *[[Special:Upload]] List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
-*LOGIN AND GO TO YOUR SANDBOX.
-*'''NOTE THE LAYOUT OF YOUR SANDBOX PAGE''':
-**First is a box telling others about your reservation and instructions not to delete.
-**Next is a title 'Your Problem Set Scenes'.
-**ON THE RIGHT and below the line under the title text is the 3D Jmol applet window with the 1d66 structure spinning in it.
-**Finally, TO THE LEFT of the Jmol applet window is information instructing you how to specify a scene in the 3D applet window at the right.
-*First to let everyone know this is your page and starting setting it up for the format it will need to be in when you turn in your problem set, you'll edit your Sandbox to have your name in place of "Your" in front of "Problem Set Scenes":
-**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''':
-***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 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.
-***Finally, there is the text that tells the page how to display the instructions I set up for you. We will return to this block of text later.
-**For now we are just going to change the 'Your' in the title text to read the possessive of your name, for example the line specifying the title on my page would read:<br> <nowiki>==Wayne Decatur's Problem Set Scenes==</nowiki>
-**Once you have change the text in the editing window, look below the editing window (you may need to scroll your browser page down), and click the 'Save Page' button.
-**'''Congratulations, you just edited your first Proteopedia page!'''
 *[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
-*'''Now author a scene (view) to add to your Sandbox page''':
+*[[User:Wayne Decatur/Biochem642 Sandbox Steps|Perform basic editing and creation of scenes in your Sandboxes]]
-**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.
-**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 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.
-**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 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.
-**
-*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.
-**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.
-*Add this scene as a new 3D Jmol applet window on the same page:
-**Copy the original applet
 *[[Help:Copying FirstGlance Scenes into Proteopedia|Copying FirstGlance Scenes into Proteopedia]]
 *Proteopedia pages can be exported for offline viewing using the toolbox on the left.
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 *[[Proteopedia:Video Guide]]
 *[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
-*[[User:Wayne Decatur/SandboxTransitionExample|Example of scenes without and with transitions]]
+<!--*[[User:Wayne Decatur/SandboxTransitionExample|Example of scenes without and with transitions]]-->
 *[[User:Tom Gluick/glutamine synthetase]] (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
+*[http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Reference Manual] for advanced scene authoring in Jmol using commands because [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#directscripting direct scripting works for Proteopedia too].
 *[http://www.bioinformatics.org/jmol-tutorials/wiki/ Comparison of Jmol tutorial-authoring systems]
-*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting Taking a View in FirstGlance in Jmol and making a Proteopedia Scene]
+*[[Help:Copying FirstGlance Scenes into Proteopedia|Copying FirstGlance in Jmol Scenes into Proteopedia]]
-*[[Help:Copying FirstGlance Scenes into Proteopedia|Copying FirstGlance Scenes into Proteopedia]]
 *[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed [[Help:Copying FirstGlance Scenes into Proteopedia|here]] or at [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting the JTAT site on extracting state scripts], it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
-*[http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Reference Manual] for advanced scene authoring in Jmol using commands because [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#directscripting direct scripting works for Proteopedia too].
 *[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/index.htm Jmol Tutorial-Authoring Template (JTAT)] describes and works for developing and viewing scenes offline or developing and viewing privately.
+*[[Morphs|Morphing]] allow displaying the visual transition between two molecular conformations.
 *[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms.
 *[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making.