User:Wayne Decatur/Biochem642 Molecular Visualization Sessions
IntroductionIntroduction
- Nobel prizes 2009 studies of the structure and function of the ribosome structure.
- Structures:
- X-ray crystallography and resolution
- NMR
- Cryo-EM
- Theoretical Models
- The Protein Data Bank
- PDB Statistics
- search 1d66 - display text of PDB file
- MolviZ "Top 5" item III shows us how we can explore structures.
- FirstGlance in Jmol
- Proteopedia allows viewing scenes, as well as creating and saving scenes. Hosts a lot of resources in information too.
- Example of resources and information: About Macromolecular Structure
- Searching: 2 means - example net charge
Viewing StructuresViewing Structures
- Proteopedia: 1d66
- Spin
- Quality toggle
- Popup
- Conservation: 5cyt, explanation, and see also The ConSurf Database and The ConSurf Server (Note: This is also item IV at MolviZ "Top 5".)
- FirstGlance in Jmol from 1d66 entry in Proteopedia
- Views and Convenience buttons
- How many chains?
- 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
- Labels
- N→C Rainbow
- Composition
- Cartoon
- Charge/Hydrophobic
- Slab
- 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
- Gaps - I'd suggest helpful PDBSum linked to at Proteopedia vs. less clear Sequence at PDB or S2C (compare 2ace)
- More Views
- Distance measuring
- Cation-Pi interactions (salt bridges come up first)
- Reset, Snapshot Gallery
- Contacts
- Views and Convenience buttons
- 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 MolviZ "Top 5".)
Authoring pages and scenesAuthoring pages and scenes
- Proteopedia:Video Guide
- How to edit pages in Proteopedia → Example 1, example 2, and 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.
- NOTE THE LAYOUT OF YOUR SANDBOX PAGE:
- First is a box telling others about your reservation and instructions not to delete.
- Next is a title 'Your Problem Set Scenes'.
- ON THE RIGHT and below the line under the title text is the 3D Jmol applet window with 1d66 spinning in it.
- Finally, TO THE LEFT of the Jmol applet window is information instructing you how to specify a scene in the 3D applet window at the right.
- First to let everyone know this is your page and starting setting it up for the format it will need to be in when you turn in your problem set, you'll edit your Sandbox to have your name in place of "Your" in front of "Problem Set Scenes":
- Click on 'edit this page' up at the top of the page.
- NOTE THE LAYOUT OF YOUR SANDBOX PAGE EDITING PAGE AND HOW IT IS CONTROLLING WHAT YOU SEE ON THE PAGE:
- First is a line that is template telling others about your reservation and instructions not to delete.
- Next is the text of the title you saw which is in between some equal signs that just signals in wiki-talk, called wikitext, how that text is to be formatted special.
- Next is wikitext beginning with '<applet' and ending by being closed with '/>'. All the text between '<applet' and '>/' just specifies the parameters of how to set up and what to show in the Jmol applet window where you saw 1d66 spinning.
- Finally, there is the text that tells the page how to display the instructions I set up for you. We will return to this block of text later.
- For now we are just going to change the 'Your' in the title text to read the possessive of your name, for example the line specifying the title on my page would read:
==Wayne Decatur's Problem Set Scenes== - Once you have change the text in the editing window, look below the editing window (you may need to scroll your browser page down), and click the 'Save Page' button.
- Congratulations, you just edited your first Proteopedia page!
- Note that at the end of this block of text and flanked my nowiki tags to tell the page not to process it as normal wikitext is wikitext very similar to what we just saw above; however, there is a significant difference: the scene parameter has been added in front of the caption parameter. In between the single quotes is the name of a dummy scene; there is no real scene corresponding to this name.
- Proteopedia's Scene Authoring Tools
- Load molecule: 1d66
- Make a scene (view) and add it to your Sandbox page.
- Make that scene show in the 3D applet window when the page comes up:
- BEFORE YOU OPEN EDIT, read the process on the normal page which I left for you. This part will remain untouched, at least for now.
- Click 'EDIT THIS PAGE', and add a scene tag to the 3D applet window information by copying the sample one (that generates the text you read from the page when not in editing mode) and putting it in the real one above. The one you pasted isn't a real scene name though! You need to get your scene information there.
- So copy the name of your scene between the single quotes down lower on the page, and replace the dummy text between the single quotes of the scene tag you just added to the 3D applet window information.
- Load that same scene again in the Scene Authoring Tools using the load scene tab, modify it, and save a new scene. Paste the scene into your page.
- Add this scene as a new 3D window on the same page:
- Copy the original applet
- Copying FirstGlance Scenes into Proteopedia
- Proteopedia pages can be exported for offline viewing using the toolbox on the left.
ResourcesResources
Molecular VisualizationMolecular Visualization
- About Macromolecular Structure
- Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
- MolviZ "Top 5"
- MolviZ.Org
- Protein Explorer's Glossary
- Eric Martz's recent workshop at his list of workshops.
- Jmol Application
- PyMol
- Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
- Swiss-pdb Viewer a.k.a Deep View
- Protein Explorer
Authoring Scenes and Views in Proteopedia and beyondAuthoring Scenes and Views in Proteopedia and beyond
- Proteopedia:Video Guide
- Proteopedia's Scene Authoring Tools
- 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.
- Comparison of Jmol tutorial-authoring systems
- Taking a View in FirstGlance in Jmol and making a Proteopedia Scene
- Copying FirstGlance Scenes into Proteopedia
- Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed here or at 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.
- Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
- Jmol Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
- Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
- eMovie,a PyMol plug-in for macromolecular movie-making.