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***[[Help:Searching|Searching]]: 2 means - example net charge
***[[Help:Searching|Searching]]: 2 means - example net charge


==Viewing Strucutues==
==Viewing Structures==
*[[Main Page|Proteopedia]]: [[1d66]]
*[[Main Page|Proteopedia]]: [[1d66]]
**Conservation: [[5cyt]], explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server]
**Spin
**Quality toggle
**Quality toggle
**Popup
**Popup
**Conservation: [[5cyt]], explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server] (Note: This is also item IV at [http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"].)
**FirstGlance in Jmol from [[1d66]] entry in Proteopedia
**FirstGlance in Jmol from [[1d66]] entry in Proteopedia
***Views and Convenience buttons
***Views and Convenience buttons
****How many chains?
****How many chains?
****Spin
****Spin
****Hover (special to FirstGlance is ability to click and display identity; hover more general in Jmol. Model number would be shown if more than 1.)
****Water
****Water
****Labels
****Labels
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****Charge/Hydrophobic
****Charge/Hydrophobic
****Slab
****Slab
****Be aware when Ligands are on or off; ligands are often interesting moieties in the structure.
****Turn slab off and hit cartoon again. Where are the Ligands? Be aware when Ligands are on or off; ligands are often interesting moieties in the structure.
***Center atom
***Center atom
***Gaps - also use Sequence at PDB
***Gaps - I'd suggest helpful PDBSum linked to at Proteopedia vs. less clear Sequence at PDB or S2C (compare 2ace)
***More Views
***More Views
****Distance measuring
****Distance measuring
****Cation-Pi interactions
****Cation-Pi interactions (salt bridges come up first)
***Reset, Snapshot Gallery
***Contacts
***Contacts


*[http://polyview.cchmc.org/polyview3d.html Polyview-3D] for when you need an animation or extremely high-quality (most times the high quality button on Jmol is sufficient) static image.
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D] for when you need an animation or extremely high-quality (most times the high quality button on Jmol is sufficient) static image. (Note: This is also item V at [http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"].)


==Authoring pages and scenes==
==Authoring pages and scenes==
*[[Proteopedia:Video Guide]]
*[[Proteopedia:Video Guide]]
*[[Help:Editing|How to edit pages in Proteopedia]]
*[[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]]
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*LOGIN AND GO TO YOUR SANDBOX
*[[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.
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*[http://www.umass.edu/molvis/workshop/osaka09m.htm Eric Martz's recent workshop] at [http://workshops.molviz.org his list of workshops].
*[http://www.umass.edu/molvis/workshop/osaka09m.htm Eric Martz's recent workshop] at [http://workshops.molviz.org his list of workshops].
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jmol_app.htm Jmol Application]
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jmol_app.htm Jmol Application]
*Pymol
*[http://pymol.org/ PyMol]
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy Pymol views and animations made super easy.
*[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.
*Swiss-pdb Viewer a.k.a Deep View
*Swiss-pdb Viewer a.k.a Deep View
*Protein Explorer
*Protein Explorer
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*[[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://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 Pymol views and animations made super easy.
*[[Morphs|Morphing]] allow displaying the visual transition between two molecular conformations.
*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a PyMOL plug-in for macromolecular movie-making.
*[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.


==Class Sandboxes==
==Class Sandboxes==
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