Sandbox423

From Proteopedia

Revision as of 16:33, 29 March 2012

This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!

Spring 2012 Chem423 Team Projects

Understanding the chemical basis of disease and life processes

Follow instructions posted at Student Projects for UMass Chemistry 423 Spring 2012.

Presentation Dates, Teams, Topics, and Links

3. Ryan Deeney, Jeffrey Boerth, Kate Liedell, Rebecca Bishop - Diabetes 3loh (insulin receptor) also consider 3loh Presentation 3/28/12 Draft due 3/21

6. Greg Keohane, Nicole Hofstetter, Gina Lein, Louis Pires, - cisplatin, 1a84 Presentation 4/9/12 Draft due 4/2

4. Julia Tomaszewski, Sam Kmail, Nicole Bundy, Jesse Guillet - restriction enzyme/DNA complex, 1rva Presentation 4/11/12 Draft due 4/4

5. Alec Gramann, William Frantz, Felix Alfonso, Paula Preap - Bone Formation & Apoptosis & 1m4u Presentation 4/23/12 Draft due 4/16

9. Di Lin, Jill Moore, Austin Virtue, Alexander Way - Caspase 3, 1RHK Presentation 4/23/12 Draft due 4/16

1. Jessica Royal, Anh Huynh, Stephanie Bristol, Emily Brackett - Catechol-O-methyltransferase, 2ZVJ, Parkinson's disease Presentation 4/25/12 Draft due 4/18

8. Max Nowak, Kyle Reed, Kevin Dillon, Chris Carr - dementia 1JVQ Presentation 4/25/12 Draft due 4/18

2. William Yarr, Ryan Colombo, Joey Nguyen, Jacqueline Pasek-Allen - Hemoglobin 1qxd Presentation 4/27/12 Draft due 4/20

7. Polina Berdnikova, James Hamblin, Jill Carlson, Brett Clinton - phosphatase inhibitor complexes-1nny Presentation 4/27/12 Draft due 4/20

10. Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley - leadzyme, 1nuv Presentation 4/30/12 Draft due 4/23

Xuni Li - examples

Questions & Answers

Here is a place to post questions and answers for each other about how to do things in Proteopedia. Here are some from me and previous students.

• For step-by-step instructions on creating example scenes, try Proteopedia:DIY:Scenes.
• Safari currently not working for making a scene... LKT 2/27 But it just worked for Xuni! Test saving a simple scene first.

• A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).

• To show the biological unit, follow directions at Biological Unit: Showing. The pdb file will display the "asymmetric unit" = the smallest unit that can be replicated to generate the full crystal. Example: the protein may function as a dimer (you need biochemical experiments to tell you this -- crystallography and NMR won't tell you), but the pdb file may display a monomer (if the dimer is symmetric) or two dimers (if they have slightly different conformations in the crystals -- perhaps due to crystal contacts or perhaps representing 2 functional states of the protein!).

• Anyone know what format we should be putting our references in?

For references, follow the format used in the example on the Asp receptor and they will be put in automatically. You just find out the PMID code (listed in pubmed for example) and insert it into the following, at the place where you want the reference cited (click edit to see what is actually inserted here). ^[1] You also need to add the section:

References

1. ↑ Yeh JI, Biemann HP, Pandit J, Koshland DE, Kim SH. The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding. J Biol Chem. 1993 May 5;268(13):9787-92. PMID:8486661

• Hey guys this is just a useful tip:

If you get an xml error after you try to save your changes it is due to the green scene coding. Our group experienced this issue and it would not let us access our sandbox. In order to fix this go back (or find the page to edit in your history) and delete the green scene code that was just entered. Then save the page and you should be back to your sandbox. This may be trivial to many, but just throwing it out there.

• To highlight some interesting portion of your protein:

Under the selections tab, you can "limit to residue numbers." So for example enter in 60-65, then click "replace selection" below. Then if you go to the colors tab you can pick a color for just the residues you have selected. If it is a loop or if they are hard to see you can go to the representation tab and set selection to ball and stick or spacefill.

It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.

Tips from feedback/edits of your Proteopedia Projects

Each section should start with the line that inserts the Jmol scene: then each scene for that section will appear in that window, along side your text (which should only extend 1-2 lines beyond the jmol window).

Every jmol window should have a caption so we know what we are looking at (include the name of the molecule and pdb code) Replace "insert caption here' with 'your caption'. This didn't work for me when the jmol window was not part of this section. Since you can have captions in every section, you can all make cool scenes & captions for consideration for the Molecular Playground.

Feel free to you work together on sections and add people to the credits if that helps to make a coherent and organized story.