User:Wayne Decatur/SandboxTeachingInfo
From Proteopedia
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'''SAVE OFTEN!'''<br> | '''SAVE OFTEN!'''<br> | ||
| - | ===Advanced Jmol=== | + | ===Advanced Jmol Scripting=== |
*[http://chemapps.stolaf.edu/jmol/docs/ Jmol interactive scripting documentation] | *[http://chemapps.stolaf.edu/jmol/docs/ Jmol interactive scripting documentation] | ||
| + | *[http://jmol.sourceforge.net/docs/ Jmol documentation, features illustrated and detailed surface options] | ||
===Advanced Jmol=== | ===Advanced Jmol=== | ||
*[[Teaching Scenes, Tutorials, and Educators%27 Pages]] | *[[Teaching Scenes, Tutorials, and Educators%27 Pages]] | ||
*[[Student Projects]] | *[[Student Projects]] | ||
Revision as of 01:04, 21 November 2008
Contents |
Proteopedia and Authoring Pages for your Projects
Introduction
Types of pages
- Proteopedia:Topic Pages
- Lac repressor at Proteopedia is an example of a topic page.
- [on seeded vs. topic pages at Proteopedia]
- 1rpu is a seeded page.
- 1eve is a seeded page that had been expanded.
- Help:Searching
- User:Eric Martz is a user page at only he can edit.
- Special:RequestAccount
- User:Eric Martz/Nucleosomes is a protected page that is a subpage of a user. It is authored by that user and only editable by that user.
- User:Wayne Decatur
- User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing is another example if a protected user subpage.
- Help:Protected Pages tells how to create protected as subpages of your user page.
Authoring pages
Authoring scenes within pages
- Molecular Scene Authoring Tools
- User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
Advanced Scene Authoring
- Scripting molecular views directions as found a Jmol Tutorial Authoring Tools talks about the variations you can use to get your desired scene; see the next entry as well.
- Scripting in FirstGlance in Jmol directions as found a Jmol Tutorial Authoring Tools (JTAT) also has more information on going from scenes generated in FirstGlance in Jmol to a state script and this approach can be adapted to going from FirstGlance in Jmol scenes to Proteopedia scenes, the important point being to be use consistent version of Jmol.
- Jmol Protein Explorer's pwoerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed at 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 slight discrepancies.
Be prepared to do some troubleshooting to get the exact scene you need. Keep in mind this an evolving and improving system and that some means of generating aspects of scenes outside of Proteopedia's Scene authoring tools might not be saved in the scene information properly by Proteopedia's Scene Authoring Tools. I have found this to be the case with instances involving representations that use 'surfaces', 'dots', and 'configuration' settings. For the problematic instance I mention, I found that troubleshooting simply involved either using a state script or Proteopedia's own Scene Authoring Tools to get close to the scene I want and then using the Jmol console to execute the problematic commands bypasses the errors I was encountering.
SAVE OFTEN!
Advanced Jmol Scripting
- Jmol interactive scripting documentation
- Jmol documentation, features illustrated and detailed surface options
