Sandbox423: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Lynmarie K Thompson, Student, Joe Perito, Louis Pires, Arash Manafirad

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 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.'''
+'''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar,
+Emily Boyle,
+Nicole Kirby,
+Cory Thomas,
+Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq)
+'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard,
+Annie Burton,
+Jianlong Li,
+Daniel Marco,
+Nathaniel Park -- Drug intercalation complex of DNA (1xcs)
+'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni,
+Robert Green,
+Uday Prakhya,
+Nicholas Rivelli,
+Elizabeth Swanson -- Vitamin D binding protein (1j7e)
+'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker,
+Kate Daborowski,
+Patrick Murphy,
+Benjamin Rizkin,
+Aaron Thole -- Vitamin D receptor/vitamin D (1db1)
+'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter,
+Samuel Pierce,
+Hyunjoon Choi,
+Anton El Khoury,
+Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor)  (2jch)
+'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker,
+Lauren Timmins,
+Aidan Finnerty,
+Adam Murphy,
+Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj)
+'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand,
+Elizabeth Humble,
+Kati Johnson,
+Samantha Kriksceonaitis,
+Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g)
+'''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley,
+Katie Kwan,
+Daniel Peters,
+Ishtiaque Rafiyu,
+Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl)
+'''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park,
+Daniel Estabrook,
+Marissa Burgess,
+Miranda Goldman,
+Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly)
+'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler,
+Patrick Tonne,
+Owen O'Connor,
+Tyler Russell,
+Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG)
 == Examples ==
-See [[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
+See
-[[Student_Projects_for_UMass_Chemistry_423_Spring_2015]]
-[[Student_Projects_for_UMass_Chemistry_423_Spring_2012]]
+[[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]]
-[[Student_Projects_for_UMass_Chemistry_423_Spring_2011]]
+[[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]]
+[[Student_Projects_for_UMass_Chemistry_423_Spring_2011#Project Teams, Topics, Links, and Presentation Dates|2011 Team Projects]]
 ==Help==
 See  [[Student Projects for UMass Chemistry 423 Spring 2016|Help]]
-===Questions & Answers===
+==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
+. always use "replace selection” to be sure you aren’t bringing along some other selection, and also use “hide selection” under representations.
+. 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