User:Wayne Decatur/SandboxTeachingInfo: Difference between revisions

(11 intermediate revisions by the same user not shown)

Line 1:

==Proteopedia and Authoring Pages for your ~~Projects~~==

==Proteopedia and Authoring Pages for your Presentations==

===Introduction===

*[http://en.wikipedia.org/wiki/Lac_repressor Lac Repressor at Wikipedia]

Line 6:

*[http://molvis.sdsc.edu/fgij/fg.htm?mol=1RPU FirstGlance in Jmol]

*[[Lac repressor|Lac repressor at Proteopedia]]

*''Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules'', Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. [http://genomebiology.com/2008/9/8/R121 ''Genome Biology'' 9:R121, August 2008] or [http://dx.doi.org/10.1186/gb-2008-9-8-r121 doi:10.1186/gb-2008-9-8-r121]

===Types of pages===

*[[Proteopedia:Topic Pages]]

*[[Lac repressor|Lac repressor at Proteopedia]] is an example of a topic page.

*[[http://proteopedia.org/wiki/VideoGuide/ProteopediaVideoGuide3/ProteopediaVideoGuide3.htm|Video on seeded vs. topic pages at Proteopedia]]

*[http://proteopedia.org/wiki/VideoGuide/ProteopediaVideoGuide3/ProteopediaVideoGuide3.htm|Video on seeded vs. topic pages at Proteopedia]

*[[1rpu]] is a seeded page.

*[[1eve]] is a seeded page that had been expanded.

Line 17:

Line 18:

*[[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.

*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example of a protected user subpage.

*[[Help:Protected Pages]] tells how to create protected as subpages of your user page.

*[[Help:Protected Pages]] tells how to create protected subpages of your user page.

*[[Teaching Strategies Using Proteopedia]] describes using temporary sandbox pages for practice or experimenting or colloboration.

===Authoring pages===

*[[Proteopedia:Video Guide|Movies Showing How to Author Proteopedia Pages]]

Line 24:

Line 26:

===Authoring scenes within pages===

*[[Scene authoring tools|Molecular Scene Authoring Tools]]

*[[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.

===Advanced Scene Authoring===

*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#scripting 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.

*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting 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.

*[http://chemapps.stolaf.edu/pe/protexpl/ 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.

*[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 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.

'''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 'isosurface', 'dots', and 'configuration' settings. For the problematic instances 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.

<br>

'''SAVE OFTEN!'''<br>

===Advanced Jmol===

===Advanced Jmol Scripting===

*[http://chemapps.stolaf.edu/jmol/docs/ Jmol interactive scripting documentation]

===~~Advanced Jmol~~===

*[http://jmol.sourceforge.net/docs/ Jmol documentation, features illustrated and detailed surface options]

===Other student projects and teaching resources in Proteopedia===

*[[Student Projects]]

*[[Teaching Strategies Using Proteopedia]]

*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]

*[[~~Student Projects~~]]

*[[User:Jaime Prilusky/Sandbox quiz |Quizzes with Proteopedia]]

@@ Line 1: / Line 1: @@
-==Proteopedia and Authoring Pages for your Projects==
+==Proteopedia and Authoring Pages for your Presentations==
 ===Introduction===
 *[http://en.wikipedia.org/wiki/Lac_repressor Lac Repressor at Wikipedia]
@@ Line 6: / Line 6: @@
 *[http://molvis.sdsc.edu/fgij/fg.htm?mol=1RPU FirstGlance in Jmol]
 *[[Lac repressor|Lac repressor at Proteopedia]]
+*''Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules'', Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman.  [http://genomebiology.com/2008/9/8/R121 ''Genome Biology'' 9:R121, August 2008] or [http://dx.doi.org/10.1186/gb-2008-9-8-r121 doi:10.1186/gb-2008-9-8-r121]
 ===Types of pages===
 *[[Proteopedia:Topic Pages]]
 *[[Lac repressor|Lac repressor at Proteopedia]] is an example of a topic page.
-*[[http://proteopedia.org/wiki/VideoGuide/ProteopediaVideoGuide3/ProteopediaVideoGuide3.htm|Video on seeded vs. topic pages at Proteopedia]]
+*[http://proteopedia.org/wiki/VideoGuide/ProteopediaVideoGuide3/ProteopediaVideoGuide3.htm|Video on seeded vs. topic pages at Proteopedia]
 *[[1rpu]] is a seeded page.
 *[[1eve]] is a seeded page that had been expanded.
@@ Line 17: / Line 18: @@
 *[[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.
+*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example of a protected user subpage.
-*[[Help:Protected Pages]] tells how to create protected as subpages of your user page.
+*[[Help:Protected Pages]] tells how to create protected subpages of your user page.
+*[[Teaching Strategies Using Proteopedia]] describes using temporary sandbox pages for practice or experimenting or colloboration.
 ===Authoring pages===
 *[[Proteopedia:Video Guide|Movies Showing How to Author Proteopedia Pages]]
@@ Line 24: / Line 26: @@
 ===Authoring scenes within pages===
 *[[Scene authoring tools|Molecular Scene Authoring Tools]]
+*[[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.
 ===Advanced Scene Authoring===
 *[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#scripting 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.
 *[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting 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.
-*[http://chemapps.stolaf.edu/pe/protexpl/ 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.
+*[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 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.
+'''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 'isosurface', 'dots', and 'configuration' settings.  For the problematic instances 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.
 <br>
 '''SAVE OFTEN!'''<br>
-===Advanced Jmol===
+===Advanced Jmol Scripting===
 *[http://chemapps.stolaf.edu/jmol/docs/ Jmol interactive scripting documentation]
-===Advanced Jmol===
+*[http://jmol.sourceforge.net/docs/ Jmol documentation, features illustrated and detailed surface options]
+===Other student projects and teaching resources in Proteopedia===
+*[[Student Projects]]
+*[[Teaching Strategies Using Proteopedia]]
 *[[Teaching Scenes, Tutorials, and Educators%27 Pages]]
-*[[Student Projects]]
+*[[User:Jaime Prilusky/Sandbox quiz |Quizzes with Proteopedia]]