User:Wayne Decatur/NASCE2011 - Revision history

Wayne Decatur: /* Macromolecular Visualization */

2013-11-05T14:06:20Z

Macromolecular Visualization

← Older revision		Revision as of 14:06, 5 November 2013
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	*[[About Macromolecular Structure]]		*[[About Macromolecular Structure]]
	*[http://molvis.sdsc.edu/fgij/ FirstGlance in Jmol] is very useful for exploring PDB entries or upload structure files.		*[http://molvis.sdsc.edu/fgij/ FirstGlance in Jmol] is very useful for exploring PDB entries or upload structure files.
			*[http://biomodel.uah.es/en/scale/ Easily compare the size of macromolecules easily with this page]. It works on any device because it has both a Java-based and javascript-based option.
	*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate useful views. This effort is building Chime-based Protein Explorer to work with Jmol, and a few features may still not yet work.		*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate useful views. This effort is building Chime-based Protein Explorer to work with Jmol, and a few features may still not yet work.
	*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"]		*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"]

Wayne Decatur at 13:20, 30 October 2013

2013-10-30T13:20:56Z

← Older revision		Revision as of 13:20, 30 October 2013
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	*RNA-protein modeling		*RNA-protein modeling
	**The [http://iimcb.genesilico.pl/index.php/software.html software page at the Bujnicki Laboratory website] hosts software for determining two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking. See the companion [http://www.biomedcentral.com/1471-2105/12/348 article].		**The [http://iimcb.genesilico.pl/index.php/software.html software page at the Bujnicki Laboratory website] hosts software for determining two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking. See the companion [http://www.biomedcentral.com/1471-2105/12/348 article].
			==References==
			<references/>
	==Class Sandboxes==		==Class Sandboxes==
	{\|		{\|

Wayne Decatur: /* Small Molecule Visualization and Model Kits */ Added JSME

2013-10-30T13:19:10Z

Small Molecule Visualization and Model Kits: Added JSME

← Older revision		Revision as of 13:19, 30 October 2013
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	===Small Molecule Visualization and Model Kits===		===Small Molecule Visualization and Model Kits===
	*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses JSmol ~~that is being developed~~		*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses JSmol
			*[http://biomodel.uah.es/en/DIY/JSME/ JSME Molecular Editor] - , the non-Java alternative to JME; uses JSmol <ref>B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) [http://www.jcheminf.com/content/5/1/24 article]</ref>
	*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers		*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers
	*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items.		*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items.

Wayne Decatur: /* Small Molecule Visualization and Model Kits */

2012-11-30T15:06:47Z

Small Molecule Visualization and Model Kits

← Older revision		Revision as of 15:06, 30 November 2012
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	===Small Molecule Visualization and Model Kits===		===Small Molecule Visualization and Model Kits===
	*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses ~~JSMOL~~ that is being developed		*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses JSmol that is being developed
	*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers		*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers
	*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items.		*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items.

Wayne Decatur: /* Small Molecule Visualization and Model Kits */

2012-11-30T15:01:20Z

Small Molecule Visualization and Model Kits

← Older revision		Revision as of 15:01, 30 November 2012
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	===Small Molecule Visualization and Model Kits===		===Small Molecule Visualization and Model Kits===
	*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit]		*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses JSMOL that is being developed
			*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers
	*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items.		*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items.
	*[http://chemcanvas.sourceforge.net/chemWin.html ChemCanvas, an open source chemical diagram editor]		*[http://chemcanvas.sourceforge.net/chemWin.html ChemCanvas, an open source chemical diagram editor]

Wayne Decatur at 16:46, 8 November 2012

2012-11-08T16:46:31Z

← Older revision		Revision as of 16:46, 8 November 2012
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	*[[Help:Getting Started in Proteopedia]]		*[[Help:Getting Started in Proteopedia]]
	*User or Sandbox login		*User or Sandbox login
	*We encourage you all to become users of any sort. If you become a registered, you can save information in your userspace regardless of your overall contribution to public spaces.		*We encourage you all to become users of any sort. If you become a registered user, you can save information in your userspace regardless of your overall contribution to public spaces.

	==Types of Proteopedia pages==		==Types of Proteopedia pages==

Wayne Decatur: /* Types of Proteopedia pages */

2012-05-09T14:34:40Z

Types of Proteopedia pages

← Older revision		Revision as of 14:34, 9 May 2012
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	*PDB Entry Pages		*PDB Entry Pages
	*User space Pages		*User space Pages
	*Sandbox Pages		*Sandbox Pages , see [[Help:Sandboxes]]
	*Workbench Pages -		*Workbench Pages ,see [[Proteopedia:Workbench]] and [[Group:SMART:Workbench_SMART_Teams#]]
	**[[Proteopedia:Workbench]]
	**[[Group:SMART:Workbench_SMART_Teams#]]
	*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]]		*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]]
	*Administrative		*Administrative

Wayne Decatur: /* Types of Proteopedia pages */

2012-05-09T14:32:53Z

Types of Proteopedia pages

← Older revision		Revision as of 14:32, 9 May 2012
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	*PDB Entry Pages		*PDB Entry Pages
	*User space Pages		*User space Pages
	*Sandbox Pages		*Sandbox Pages
	*Workbench Pages		*Workbench Pages -
			**[[Proteopedia:Workbench]]
			**[[Group:SMART:Workbench_SMART_Teams#]]
	*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]]		*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]]
	*Administrative		*Administrative

Wayne Decatur: /* Small Molecule Visualization and Model Kits */ added CheS-mapper

2012-03-29T13:05:55Z

Small Molecule Visualization and Model Kits: added CheS-mapper

← Older revision		Revision as of 13:05, 29 March 2012
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	*[http://chemapps.stolaf.edu/jmol/docs/examples-12/ChemDoodleWeb/samples/sketcher_Jmol.html ChemDoodleWeb Integrated with Jmol]		*[http://chemapps.stolaf.edu/jmol/docs/examples-12/ChemDoodleWeb/samples/sketcher_Jmol.html ChemDoodleWeb Integrated with Jmol]
	*[http://librairiedemolecules.education.fr/outils/scribmol/ Scribmol] is a ChemDoodleWeb Integrated with Jmol application found at [http://librairiedemolecules.education.fr/outils/ a utilities page] (french) with other useful visualization tools.		*[http://librairiedemolecules.education.fr/outils/scribmol/ Scribmol] is a ChemDoodleWeb Integrated with Jmol application found at [http://librairiedemolecules.education.fr/outils/ a utilities page] (french) with other useful visualization tools.
			* [http://opentox.informatik.uni-freiburg.de/ches-mapper/ CheS-Mapper (Chemical Space Mapper)] is a 3D-viewer for chemical datasets with small compounds. It on the fly divides large datasets into clusters of similar compounds, arranging them in 3D space, such that their spatial proximity reflects their similarity. It is an open-source Java application, based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R.

	===Topic Pages - Education===		===Topic Pages - Education===

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

2012-03-27T14:22:44Z

Authoring Scenes and Views in Proteopedia and beyond

← Older revision		Revision as of 14:22, 27 March 2012
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	===Authoring Scenes and Views in Proteopedia and beyond===		===Authoring Scenes and Views in Proteopedia and beyond===
	*[[Proteopedia:Video Guide]]		*[[Proteopedia:Video Guide]]
			* [[Help:Getting Started in Proteopedia]]
	* [[Proteopedia:How to Make a Page]]		* [[Proteopedia:How to Make a Page]]
	*[[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.
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	*[[Morphs\|Morphing]] allows displaying the visual transition between two molecular conformations.		*[[Morphs\|Morphing]] allows 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.


	===Modeling===		===Modeling===