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 2015 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 2015]].
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Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2016]].
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==='''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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1. Team members: topic name - [[Sandbox Reserved 425|pdbcode]]
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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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2. Team members: topic name - [[Sandbox Reserved 426|pdbcode]]
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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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3. Team members: topic name - [[Sandbox Reserved 427|pdbcode]]
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'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard,
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Annie Burton,
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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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4. Team members: topic name - [[Sandbox Reserved 428|pdbcode]]
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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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5. Team members: topic name - [[Sandbox Reserved 429|pdbcode]]
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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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6. Team members: topic name - [[Sandbox Reserved 430|pdbcode]]
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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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7. Team members: topic name - [[Sandbox Reserved 431|pdbcode]]
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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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8. Team members: topic name - [[Sandbox Reserved 432|pdbcode]]
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'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand,
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Elizabeth Humble,
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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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9. Team members: topic name - [[Sandbox Reserved 433|pdbcode]]
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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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10. Team members: topic name - [[Sandbox Reserved 434|pdbcode]]
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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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== Project Instructions ==
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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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== Examples ==
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See
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'''1. Topics due Monday 2/9 11pm''
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
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:'''Teams''' of 4 people will be assigned, to include both chemistry and chemical engineering majors on most teams. You may request one teammate by emailing the TA by noon Feb 16.
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:Once you know your team assignment, select an available '''topic''' (not already chosen by another team); see our course website for suggestions and guidelines to find a simple protein-ligand complex (eg protein-drug, nucleic acid-drug, or protein-DNA) with a known structure in the pdb that interests your team. If you want to choose a topic not on the list, be sure that it does not already have a detailed Proteopedia page and email Prof Thompson to get approval: send the pdb code for the complex and briefly explain the disease connection or why it is interesting. Add your topic to the team list at [[Sandbox423]] by 2/24.
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'''2. Sandbox page displaying initial structure, description, and one green scene due by end of class workshop 2/27'''
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[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
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:'''Start your assigned sandbox page''': Find the pdb id for your protein-ligand complex in the Protein Data Bank. In your assigned sandbox page click"edit this page" (top) and follow the directions to insert your rotating structure on your page. Describe and illustrate with a green scene the secondary structure of your protein.
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'''3. Sandbox page with each section displaying an outline and at one least green scene due by beginning of class 3/5'''
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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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:'''Each team member''' should '''read the primary reference''' for the pdb structure and create an '''outline for their section''' and at least '''one green scene'''. Teams will meet during class to discuss the overall organization as needed to make it logical and avoid duplication. As individuals proceed to create their sections, they should watch the other sections and stay in contact as needed to create a coherent overall project.
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'''4. Project near-final draft, due 1 week before presentation. ''' Presentation dates will be assigned when topics are chosen. Prof Thompson will provide suggestions for improvements to your draft; you may also request feedback earlier.
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''Your proteopedia page should be organized into the following required sections, with each team member responsible for one of sections a-d of the team project.''
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Each section should have its own JMol window. Provide an interesting description (suitable for non-experts), and illustrate your points about the complex with multiple green scenes. Be concise: the written description should not extend beyond the jmol window. Do not include any copyrighted figures. All sections must be written in your own words with citations to your sources, following the reference format in the example below. You may include links to other interesting information or scenes but you must create your own scenes for display on your page.
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''Make it interesting and accessible to a non-scientist! Show clearly some chemical details to illustrate the chemistry of life processes!''
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a. Introduction
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:Introduce the protein function, how it is related to a disease, and what is important about the ligand in the complex. Make a green scene suitable for the Molecular Playground: an attractive and informative illustration of the protein complex with an interesting short caption describing it.
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b. Overall structure
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:Describe the overall structure of your protein in words and make "green scenes" to illustrate your points. What elements of secondary structure are present (ie 5 alpha helices and 2 beta strands) and how are they organized? Additional description and green scenes could illustrate the polar/nonpolar distrubution of amino acids (is the inside of the barrel polar or nonpolar?), packing of amphipathic elements, etc.
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c. Binding interactions
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:Describe features of the drug or ligand or protein-protein binding site in words and make "green scenes" to illustrate your points. Show the interactions that stabilize binding of this molecule to the protein (ie H bonds).
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d. Additional features
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:Describe and use green scenes to illustrate additional features of the macromolecule. What you do here depends on what information is available. If a structure of the protein-substrate complex is available, you could compare protein interactions with the substrate vs. with the drug. If the drug is a transition state inhibitor, explain and illustrate that (eg include a reaction scheme with structures of the substrate, transition state and product -- but don't borrow a published scheme).
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e. Credits -- at the end list who did which portion of the project:
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:Introduction -- name of team member
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:Overall structure -- name of team member
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:Drug binding site -- name of team member
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:Additional features -- name of team member
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f. References
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:This will include the published paper that describes your structure (the reference associated with your pdb code). You will get much of your information about specific interactions to look for and highlight in the structure from this reference (which is much easier than trying to find these on your own with no guidance!).
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'''4. In-class presentations on assigned dates.'''
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== Examples ==
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See [[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
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==Help==
==Help==
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See [[Student Projects for UMass Chemistry 423 Spring 2016|Help]]
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===Questions & Answers===
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==Questions & Answers==
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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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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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*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
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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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*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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*Instructions for references are at [[Help:Editing#Citing_Literature_References]].You can follow the format used in the example on the Asp receptor and they will be put in automatically.
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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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<ref>PMID: 8486661</ref>
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You also need to add the section:
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'''References'''
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<references/>
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*Hey guys this is just a useful tip:
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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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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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*If you suddenly can't get to your sandbox page (error message XML error: Mismatched tag at line 1), try [[Help:Errors]]
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===Tips from feedback/edits of past year Proteopedia Projects===
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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 (<300 words).
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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'.
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Careful with repetition of the same points in multiple sections -- instead organize the topics logically and you can have multiple people contribute to a section if you want.
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Feel free to work together on sections and add people to the credits if that helps to make a coherent and organized story.
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Follow the correct format for references, including citations in text -- see instructions and link above.
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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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Make green scenes to illustrate your points, and weave your scenes into the text.
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Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest
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Use colored text to help the reader easily see your points in the scene and to keep your text concise. For example "This view shows the <font color='red'>2 alpha helices </font> packed against the <font color='blue'> 4-stranded antiparallel beta sheet</font>." The word view would link to a scene in which the alpha helices are red and the beta sheet is blue. Go into edit mode on this page to copy the colored text section for use on your page.
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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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Avoid a list of miscellaneous facts. Choose the most interesting points to tell us in some detail and illustrate with green scenes.
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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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Tell your story with green scenes and minimal text!
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For example:
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selections: DNA, replace selection
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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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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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