User:Wayne Decatur/NASCE2011: Difference between revisions
| (9 intermediate revisions by the same user not shown) | |||
| Line 67: | Line 67: | ||
*[[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== | ||
| Line 75: | Line 75: | ||
*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#]] | ||
*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]] | *Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]] | ||
*Administrative | *Administrative | ||
| Line 167: | Line 167: | ||
*[[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"] | ||
| Line 177: | Line 178: | ||
===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 | ||
*[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://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] | ||
| Line 184: | Line 187: | ||
*[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=== | ||
| Line 191: | Line 195: | ||
===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. | ||
| Line 208: | Line 213: | ||
*[[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=== | ||
| Line 232: | Line 236: | ||
*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== | ||
{| | {| | ||