Sandbox423: Difference between revisions
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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.'' | ''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, | '''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar, | ||
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Jianlong Li, | Jianlong Li, | ||
Daniel Marco, | Daniel Marco, | ||
Nathaniel Park -- | Nathaniel Park -- Drug intercalation complex of DNA (1xcs) | ||
'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni, | '''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni, | ||
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Patrick Murphy, | Patrick Murphy, | ||
Benjamin Rizkin, | Benjamin Rizkin, | ||
Aaron Thole -- | Aaron Thole -- Vitamin D receptor/vitamin D (1db1) | ||
'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter, | '''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter, | ||
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Aidan Finnerty, | Aidan Finnerty, | ||
Adam Murphy, | Adam Murphy, | ||
Duy Nguyen -- | Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj) | ||
'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand, | '''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand, | ||
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Daniel Peters, | Daniel Peters, | ||
Ishtiaque Rafiyu, | Ishtiaque Rafiyu, | ||
Luke Ruksnaitis -- | Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl) | ||
'''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park, | '''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park, | ||
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Marissa Burgess, | Marissa Burgess, | ||
Miranda Goldman, | Miranda Goldman, | ||
Benjamin Homyak -- | Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly) | ||
'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler, | '''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler, | ||
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Owen O'Connor, | Owen O'Connor, | ||
Tyler Russell, | Tyler Russell, | ||
Nicholas Sant -- | Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG) | ||
== Examples == | == Examples == | ||
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==Help== | ==Help== | ||
See [[Student Projects for UMass Chemistry 423 Spring 2016|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). | 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 | |||