User:Wayne Decatur/Biochem642 Molecular Visualization 2010 Fall Sessions: Difference between revisions

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==Introduction==
==Introduction==
*[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ Nobel prizes 2009] studies of the structure and function of [[Ribosome|the ribosome structure]].
*Logistical information about class today and next week and problem sets
*Structures:
*Importance of Structural Biology
**X-ray crystallography and [[Resolution|resolution]]
**Important for understanding function
**NMR
**helpful representations and models for people learning
**Cryo-EM
**[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ Nobel prizes 2009] studies of the structure and function of [[Ribosome|the ribosome structure]].
**Theoretical Models
==Structural Biology for Non-structural Biologists==
*[http://www.pdb.org The Protein Data Bank]
*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"]  
**[http://www.pdb.org/pdb/static.do?p=general_information/pdb_statistics/index.html PDB Statistics]
**items III-V pertinent today
**search 1d66 - display text of PDB file
**particularly item III shows us how we can explore structures.
*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"] item III shows us how we can explore structures.
*[[Main Page|Proteopedia]] - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
**FirstGlance in Jmol
**Proteopedia allows sharing of structural biology data in a 3D, interactive manner
**Proteopedia allows viewing scenes, as well as creating and saving scenes. Hosts a lot of resources in information too.
***[[Plant Viral Protein p19 Suppression of RNA Silencing]]
***Example of resources and information: [[About Macromolecular Structure]]
***[[Glutamate receptor (GluA2)|The Glutamate Receptor (GluA2)]]
***[[Help:Searching|Searching]]: 2 means - example net charge
**Resources and information
***[[About Macromolecular Structure]]
***[[Help:Searching|Searching]]
****2 means - example search net charge


==Viewing Structures==
**Proteopedia has an entry for every PDB entry with links to useful items
*[[Main Page|Proteopedia]]: [[1d66]]
***PDB 4 digit alphanumeric accession number, similar to a PubMed ID or Genbank sequence accession number
**Spin
***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"].)
**Quality toggle
***RCSB = Protein Data Bank - use link under [[5cyt]] to RCSB
**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"].)
==Protein Data Bank==
**FirstGlance in Jmol from [[1d66]] entry in Proteopedia
* X-ray crystallography, NMR, and cryo-EM structures - total 68,840
***Views and Convenience buttons
*From FAQ: "Since October 15, 2006, PDB depositions have been restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules."
****How many chains?
*Slide on overview of crystallography, NMR, and cryo-EM structures
****Spin
*I'll point you to [http://www.umass.edu/molvis/workshop/barcel10.htm Eric Martz's recent workshop] if you seek more information in 3D-interactive examples on on resolution, temperature (b-factors, and electron density maps.
****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.)
*Display PDB file of [http://www.rcsb.org/pdb/explore/explore.do?structureId=1D66 1d66] - just a useful example of DNA-binding by a transcription factor and protein used in fusions in many genomic screens
****Water
*Under 'Links' go to Proteopedia entry for 1d66
****Labels
*Open 'FirstGlance' under 'Resources' for [[1d66]]
****N→C Rainbow
 
****Composition
==FirstGlance in Jmol==
****Cartoon
*Views and Convenience buttons
****Charge/Hydrophobic
**How many chains?
****Slab
**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.)(Another trick to see if ligand is part of a chain is to use [[Scene authoring tools|Proteopedia's Scene Authoring Tools]] and limit to chain and represent as ball and stick because covalent linkages will clearly be shown.)
****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.
**N→C Rainbow (HELP PANE)
**Charge/Hydrophobic with Slab on/off. 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 - I'd suggest helpful PDBSum linked to at Proteopedia vs. less clear Sequence at PDB or S2C (compare 2ace)
**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 (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. (Note: This is also item V at [http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"].)
==Proteopedia Scene Authoring==
*[[User:Wayne Decatur/Biochem642 Sandbox Steps|Perform basic editing and creation of scenes in your Sandboxes]]


==Authoring pages and scenes==
==Time permitting==
*[[Proteopedia:Video Guide]]
*[[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
*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*[[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.
*Proteopedia pages can be exported for offline viewing using the toolbox on the left.
*Pymol to Jmol conversion built into [[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
*Item V on [http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"] -  [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.
*[[Morphs|Morphing]] allows displaying the visual transition between two molecular conformations.
 


==Resources==
==Resources==
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*[http://www.umass.edu/microbio/chime/index.html MolviZ.Org]
*[http://www.umass.edu/microbio/chime/index.html MolviZ.Org]
*[http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/igloss.htm Protein Explorer's Glossary]
*[http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/igloss.htm Protein Explorer's Glossary]
*[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/barcel10.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]
*[http://pymol.org/ PyMol]
*[http://pymol.org/ PyMol]
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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]]
* [[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.
*[[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]]
*[[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.
<!--*[[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.
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*[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.
*[[Morphs|Morphing]] allow 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.
*[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.
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