User:Wayne Decatur/Chem791A Work Session: Difference between revisions

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*[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]]

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*[[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 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]]

*[[Help:Editing]]

*[[Special:Upload]] List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol

===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===

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*[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] 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 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.

'''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>

@@ 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]]
@@ Line 19: / Line 20: @@
 *[[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 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]]
 *[[Help:Editing]]
+*[[Special:Upload]] List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
 ===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===
@@ Line 29: / Line 33: @@
 *[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] 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 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.
+'''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>