User:Wayne Decatur/SandboxTeachingInfo: Difference between revisions
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==Teaching Proteopedia== | |||
===Introduction=== | |||
*[http://en.wikipedia.org/wiki/Lac_repressor Lac Repressor at Wikipedia] | *[http://en.wikipedia.org/wiki/Lac_repressor Lac Repressor at Wikipedia] | ||
*[http://jmol.sourceforge.net/ Jmol] | *[http://jmol.sourceforge.net/ Jmol] | ||
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*[http://molvis.sdsc.edu/fgij/fg.htm?mol=1RPU FirstGlance in Jmol] | *[http://molvis.sdsc.edu/fgij/fg.htm?mol=1RPU FirstGlance in Jmol] | ||
*[[Lac repressor|Lac repressor at Proteopedia]] | *[[Lac repressor|Lac repressor at Proteopedia]] | ||
===Types of pages=== | |||
*[[Topic Pages]] | |||
*[[Lac repressor|Lac repressor at Proteopedia is an example of a topic page]] | |||
*[[1eve]] | *[[1eve]] | ||
*[[1rpu]] | *[[1rpu]] | ||
Revision as of 03:26, 21 November 2008
Teaching ProteopediaTeaching Proteopedia
IntroductionIntroduction
Types of pagesTypes of pages
- Topic Pages
- Lac repressor at Proteopedia is an example of a topic page
- 1eve
- 1rpu
- User:Eric Martz
- User:Eric Martz/Nucleosomes
- User:Wayne Decatur
- User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing
- Help:Protected Pages
- Movies Showing How to Author Proteopedia 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.
- 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!