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.'' | ||
'''Team 1:''' Julie Boshar, | '''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, | Emily Boyle, | ||
Nicole Kirby, | Nicole Kirby, | ||
Cory Thomas, | Cory Thomas, | ||
Connor Walsh -- | Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq) | ||
'''Team 2:''' Michael Beauregard, | '''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard, | ||
Annie Burton, | Annie Burton, | ||
Jianlong Li, | Jianlong Li, | ||
Daniel Marco, | Daniel Marco, | ||
Nathaniel Park -- | Nathaniel Park -- Drug intercalation complex of DNA (1xcs) | ||
'''Team 3:''' Alex Debreceni, | '''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni, | ||
Robert Green, | Robert Green, | ||
Uday Prakhya, | Uday Prakhya, | ||
Nicholas Rivelli, | Nicholas Rivelli, | ||
Elizabeth Swanson -- | Elizabeth Swanson -- Vitamin D binding protein (1j7e) | ||
'''Team 4:''' Roger Crocker, | '''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker, | ||
Kate Daborowski, | Kate Daborowski, | ||
Patrick Murphy, | Patrick Murphy, | ||
Benjamin Rizkin, | Benjamin Rizkin, | ||
Aaron Thole -- | Aaron Thole -- Vitamin D receptor/vitamin D (1db1) | ||
'''Team 5:''' Tyler Carpenter, | '''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter, | ||
Samuel Pierce, | Samuel Pierce, | ||
Hyunjoon Choi, | Hyunjoon Choi, | ||
| Line 38: | Line 40: | ||
Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch) | Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch) | ||
'''Team 6:''' Cora Ricker, | '''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker, | ||
Lauren Timmins, | Lauren Timmins, | ||
Aidan Finnerty, | Aidan Finnerty, | ||
Adam Murphy, | Adam Murphy, | ||
Duy Nguyen -- | Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj) | ||
'''Team 7:''' Isabel Hand, | '''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand, | ||
Elizabeth Humble, | Elizabeth Humble, | ||
Kati Johnson, | Kati Johnson, | ||
Samantha Kriksceonaitis, | Samantha Kriksceonaitis, | ||
Matthew Tiller -- | Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g) | ||
'''Team 8:''' Laura Feeley, | '''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley, | ||
Katie Kwan, | Katie Kwan, | ||
Daniel Peters, | Daniel Peters, | ||
Ishtiaque Rafiyu, | Ishtiaque Rafiyu, | ||
Luke Ruksnaitis -- | Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl) | ||
'''Team 9:''' Soo Lim Park, | '''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park, | ||
Daniel Estabrook, | Daniel Estabrook, | ||
Marissa Burgess, | Marissa Burgess, | ||
Miranda Goldman, | Miranda Goldman, | ||
Benjamin Homyak -- | Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly) | ||
'''Team 10:''' Luke Schnitzler, | '''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler, | ||
Patrick Tonne, | Patrick Tonne, | ||
Owen O'Connor, | Owen O'Connor, | ||
Tyler Russell, | Tyler Russell, | ||
Nicholas Sant -- | Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG) | ||
== Examples == | == Examples == | ||
| Line 78: | Line 80: | ||
==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 | |||
Latest revision as of 17:48, 3 March 2016
This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!
Spring 2016 Chem423 Team ProjectsSpring 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)
ExamplesExamples
See
HelpHelp
See Help
Questions & AnswersQuestions & 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