Sandbox423

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'''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!'''
'''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!'''
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==''' Spring 2012 Chem423 Team Projects'''==
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==''' Spring 2016 Chem423 Team Projects'''==
'''Understanding the chemical basis of disease and life processes'''
'''Understanding the chemical basis of disease and life processes'''
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Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2012]].
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Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2016]].
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==='''Presentation Dates, Teams, Topics, and Links'''===
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''Each team should together agree upon a topic and pdb code (check the list below to be sure your topic is not already taken), then log in to Proteopedia (see instructions in Moodle) and edit this section to list your topic and pdb code.''
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3. Ryan Deeney, Jeffrey Boerth, Kate Liedell, Rebecca Bishop - [[Sandbox Reserved 427|Diabetes 3loh (insulin receptor) ]] also consider 3loh '''Presentation 3/28/12''' '''Draft due 3/21'''
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'''2/8/16 Topics are all set and copied to [[Student Projects for UMass Chemistry 423 Spring 2016]] -- notify Prof Thompson of any changes by email.'''
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6. Greg Keohane, Nicole Hofstetter, Gina Lein, Louis Pires, - [[Sandbox Reserved 430|cisplatin, 1a84 ]] '''Presentation 4/9/12''' <font color='red'>'''Draft due 4/2'''</font>
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'''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar,
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Emily Boyle,
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Nicole Kirby,
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Cory Thomas,
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Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)
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4. Julia Tomaszewski, Sam Kmail, Nicole Bundy, Jesse Guillet - [[Sandbox Reserved 428|restriction enzyme-DNA complex, 1rva]] '''Presentation 4/11/12''' <font color='red'>'''Draft due 4/4'''</font>
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'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard,
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Annie Burton,
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5. Alec Gramann, William Frantz, Felix Alfonso, Paula Preap - [[Sandbox Reserved 429| Bone Formation & Apoptosis & 1m4u ]] '''Presentation 4/23/12''' <font color='orange'>'''Draft due 4/16'''</font>
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Jianlong Li,
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Daniel Marco,
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Nathaniel Park -- Drug intercalation complex of DNA (1xcs)
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9. Di Lin, Jill Moore, Austin Virtue, Alexander Way - [[Sandbox Reserved 433|Caspase 3, 1RHK ]] '''Presentation 4/23/12''' <font color='orange'>'''Draft due 4/16'''</font>
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'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
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Robert Green,
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Uday Prakhya,
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Nicholas Rivelli,
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Elizabeth Swanson -- Vitamin D binding protein (1j7e)
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1. Jessica Royal, Anh Huynh, Stephanie Bristol, Emily Brackett - [[Sandbox Reserved 425|Catechol-O-methyltransferase, 2ZVJ, Parkinson's disease]] '''Presentation 4/25/12''' <font color='orange'>'''Draft due 4/18'''</font>
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'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker,
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Kate Daborowski,
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Patrick Murphy,
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Benjamin Rizkin,
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Aaron Thole -- Vitamin D receptor/vitamin D (1db1)
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8. Max Nowak, Kyle Reed, Kevin Dillon, Chris Carr - [[Sandbox Reserved 432|dementia 1JVQ ]] '''Presentation 4/25/12''' <font color='orange'>'''Draft due 4/18'''</font>
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'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
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Samuel Pierce,
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Hyunjoon Choi,
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Anton El Khoury,
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Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch)
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2. William Yarr, Ryan Colombo, Joey Nguyen, Jacqueline Pasek-Allen - [[Sandbox Reserved 426|Hemoglobin 1qxd ]] '''Presentation 4/27/12''' <font color='orange'>'''Draft due 4/20'''</font>
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'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker,
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Lauren Timmins,
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Aidan Finnerty,
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Adam Murphy,
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Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)
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7. Polina Berdnikova, James Hamblin, Jill Carlson, Brett Clinton - [[Sandbox Reserved 431|phosphatase inhibitor complexes-1nny]] '''Presentation 4/27/12''' <font color='orange'>'''Draft due 4/20'''</font>
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'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand,
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Elizabeth Humble,
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10. Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley - [[Sandbox Reserved 434|leadzyme, 1nuv]] '''Presentation 4/30/12''' <font color='orange'>'''Draft due 4/23'''</font>
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Kati Johnson,
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Samantha Kriksceonaitis,
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Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)
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Xuni Li - [[Sandbox Reserved 435|examples]]
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'''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley,
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Katie Kwan,
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Daniel Peters,
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Ishtiaque Rafiyu,
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Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl)
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===Questions & Answers===
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'''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park,
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Daniel Estabrook,
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Marissa Burgess,
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Miranda Goldman,
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Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)
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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.
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'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler,
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Patrick Tonne,
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Owen O'Connor,
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Tyler Russell,
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Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG)
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*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
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== Examples ==
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*<font color='red'>Safari currently not working for making a scene...</font> LKT 2/27 But it just worked for Xuni! Test saving a simple scene first.
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See
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*A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
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*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!).
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
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*Anyone know what format we should be putting our references in?
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2011#Project Teams, Topics, Links, and Presentation Dates|2011 Team Projects]]
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For references, follow the format used in the example on the Asp receptor and they will be put in automatically.
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==Help==
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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).
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See [[Student Projects for UMass Chemistry 423 Spring 2016|Help]]
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<ref>PMID: 8486661</ref>
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You also need to add the section:
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'''References'''
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==Questions & Answers==
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<references/>
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Here is a place to post new questions and answers for each other about how to do things in Proteopedia. Good tips will be added to the Help section for future classes (above link).
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*Hey guys this is just a useful tip:
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There is a recurring problem where sections below an edited section disappear (you can still see them in edit window). Don’t try to insert your scene into the command that loads the initial molecule (which may have caused the rest of the sections not to load). Write some text and then insert green scenes into text. -- Prof Thompson 2/17/16
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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.
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*To highlight some interesting portion of your protein:
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Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest
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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.
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It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.
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1. always use "replace selection” to be sure you aren’t bringing along some other selection, and also use “hide selection” under representations.
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===Tips from feedback/edits of your Proteopedia Projects===
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2. Turn on selection halos (under the structure “show selected with halos” - click the ON button). They make it much easier to keep track of what is selected, especially after multiple "invert selection" commands.
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Each section should start with the line that inserts the Jmol window: 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).
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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.
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For example:
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selections: DNA, replace selection
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Feel free to you work together on sections and add people to the credits if that helps to make a coherent and organized story.
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invert current selection (selects all but DNA)
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representations: hide selection (hides all but DNA)
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Captions in each section: cone up with a cool (short) caption that fits your best scene that you think would be good for the Molecular Playground -- something that's understandable on its own and to a broad audience.
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selections: invert selection (back to DNA)
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representations: backbone, set representation

Current revision

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

Contents

Spring 2016 Chem423 Team Projects

Understanding the chemical basis of disease and life processes

Follow instructions posted at Student Projects for UMass Chemistry 423 Spring 2016.

Each team should together agree upon a topic and pdb code (check the list below to be sure your topic is not already taken), then log in to Proteopedia (see instructions in Moodle) and edit this section to list your topic and pdb code.

2/8/16 Topics are all set and copied to Student Projects for UMass Chemistry 423 Spring 2016 -- notify Prof Thompson of any changes by email.

Team 1: Julie Boshar, Emily Boyle, Nicole Kirby, Cory Thomas, Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)

Team 2: Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, Nathaniel Park -- Drug intercalation complex of DNA (1xcs)

Team 3: Alex Debreceni, Robert Green, Uday Prakhya, Nicholas Rivelli, Elizabeth Swanson -- Vitamin D binding protein (1j7e)

Team 4: Roger Crocker, Kate Daborowski, Patrick Murphy, Benjamin Rizkin, Aaron Thole -- Vitamin D receptor/vitamin D (1db1)

Team 5: Tyler Carpenter, Samuel Pierce, Hyunjoon Choi, Anton El Khoury, Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch)

Team 6: Cora Ricker, Lauren Timmins, Aidan Finnerty, Adam Murphy, Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)

Team 7: Isabel Hand, Elizabeth Humble, Kati Johnson, Samantha Kriksceonaitis, Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)

Team 8: Laura Feeley, Katie Kwan, Daniel Peters, Ishtiaque Rafiyu, Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl)

Team 9: Soo Lim Park, Daniel Estabrook, Marissa Burgess, Miranda Goldman, Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)

Team 10: Luke Schnitzler, Patrick Tonne, Owen O'Connor, Tyler Russell, Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG)

Examples

See

2015 Team Projects

2012 Team Projects

2011 Team Projects

Help

See Help

Questions & Answers

Here is a place to post new questions and answers for each other about how to do things in Proteopedia. Good tips will be added to the Help section for future classes (above link).

There is a recurring problem where sections below an edited section disappear (you can still see them in edit window). Don’t try to insert your scene into the command that loads the initial molecule (which may have caused the rest of the sections not to load). Write some text and then insert green scenes into text. -- Prof Thompson 2/17/16

Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest

1. always use "replace selection” to be sure you aren’t bringing along some other selection, and also use “hide selection” under representations.

2. Turn on selection halos (under the structure “show selected with halos” - click the ON button). They make it much easier to keep track of what is selected, especially after multiple "invert selection" commands.

For example: selections: DNA, replace selection invert current selection (selects all but DNA) representations: hide selection (hides all but DNA) selections: invert selection (back to DNA) representations: backbone, set representation

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