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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.
*[[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  
*[[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 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 1d66 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 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.
***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 1d66 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!'''
*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.
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*Load molecule: 1d66
*[[User:Wayne Decatur/Biochem642 Sandbox Steps|Perform basic editing and creation of scenes in your Sandboxes]]
*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:
**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.
**
**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 window on the same page:
**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]]
*Proteopedia pages can be exported for offline viewing using the toolbox on the left.
*Proteopedia pages can be exported for offline viewing using the toolbox on the left.
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*[[Proteopedia:Video Guide]]
*[[Proteopedia:Video Guide]]
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*[[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.
*[[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/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/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.
*[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://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.
*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making.
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