User:Wayne Decatur/Biochem642 Molecular Visualization Sessions - Revision history

Wayne Decatur: /* Authoring Scenes and Views in Proteopedia and beyond */

2009-11-28T02:04:56Z

Authoring Scenes and Views in Proteopedia and beyond

← Older revision		Revision as of 02:04, 28 November 2009
Line 77:		Line 77:
	*[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://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.
	*[[~~Morps~~\|~~Moprhing~~]] allow displaying the visual transition between two molecular conformations.		*[[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.

Wayne Decatur at 02:24, 30 October 2009

2009-10-30T02:24:47Z

← Older revision		Revision as of 02:24, 30 October 2009
Line 77:		Line 77:
	*[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://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.
			*[[Morps\|Moprhing]] 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.

Wayne Decatur: /* Authoring Scenes and Views in Proteopedia and beyond */

2009-10-30T02:12:28Z

Authoring Scenes and Views in Proteopedia and beyond

← Older revision		Revision as of 02:12, 30 October 2009
Line 72:		Line 72:
	<!--*[[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.
	*[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.

Wayne Decatur: /* Authoring Scenes and Views in Proteopedia and beyond */

2009-10-30T02:07:54Z

Authoring Scenes and Views in Proteopedia and beyond

← Older revision		Revision as of 02:07, 30 October 2009
Line 70:		Line 70:
	*[[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://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]

Wayne Decatur: /* Authoring pages and scenes */

2009-10-29T22:46:00Z

Authoring pages and scenes

← Older revision		Revision as of 22:46, 29 October 2009
Line 49:		Line 49:
	*[[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
	*[[Scene authoring tools\|Proteopedia's Scene Authoring Tools]]		*[[Scene authoring tools\|Proteopedia's Scene Authoring Tools]]
	*[[~~Editing~~ User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]		*[[User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]
	*[[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.

Wayne Decatur: /* Authoring pages and scenes */

2009-10-29T22:34:34Z

Authoring pages and scenes

← Older revision		Revision as of 22:34, 29 October 2009
Line 48:		Line 48:
	*[[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
			*[[Scene authoring tools\|Proteopedia's Scene Authoring Tools]]
	*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]		*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]
	*[[Scene authoring tools\|Proteopedia's Scene Authoring Tools]]
	*[[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.

Wayne Decatur: /* Authoring pages and scenes */

2009-10-29T22:34:13Z

Authoring pages and scenes

← Older revision		Revision as of 22:34, 29 October 2009
Line 49:		Line 49:
	*[[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
	*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]		*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]
			*[[Scene authoring tools\|Proteopedia's Scene Authoring Tools]]
	*[[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.

Wayne Decatur: /* Authoring pages and scenes */

2009-10-29T22:30:00Z

Authoring pages and scenes

← Older revision		Revision as of 22:30, 29 October 2009
Line 48:		Line 48:
	*[[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
	*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]		*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps\|Perform basic editing and creation of scenes in your Sandboxes]]
	*[[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.

Wayne Decatur: /* Authoring pages and scenes */

2009-10-29T22:29:44Z

Authoring pages and scenes

@@ Line 48: / Line 48: @@
 *[[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
-*LOGIN AND GO TO YOUR SANDBOX.
+*[[Editing User:Wayne Decatur/Biochem642 Sandbox Steps|Perform basic editing and creation of scenes in your Sandboxes]
 *[[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.

Wayne Decatur: /* Getting wikitext or scene names for old scenes or if you forgot to copy the scene before: */

2009-10-29T22:25:56Z

Getting wikitext or scene names for old scenes or if you forgot to copy the scene before:

← Older revision		Revision as of 22:25, 29 October 2009
Line 103:		Line 103:
	===Getting wikitext or scene names for old scenes or if you forgot to copy the scene before:===		===Getting wikitext or scene names for old scenes or if you forgot to copy the scene before:===
	#Enter edit mode if you aren't in it, by pressing 'edit this page' up at the top of the page.		#Enter edit mode if you aren't in it, by pressing 'edit this page' up at the top of the page.
	##Show the Scene Authoring tools.		#Show the Scene Authoring tools.
	#Click the 'load scene' tab and use the menu to find and select the scene name and version number.		#Click the 'load scene' tab and use the menu to find and select the scene name and version number.
	#The scene will then come up in the Jmol window at the right and the wikitext will appear in the window at the bottom.		#The scene will then come up in the Jmol window at the right and the wikitext will appear in the window at the bottom.