Sandbox423
From Proteopedia
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Di Lin, Jill Moore, Austin Virtue, Alexander Way | Di Lin, Jill Moore, Austin Virtue, Alexander Way | ||
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| + | ==Questions & Answers== | ||
| + | |||
| + | 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. | ||
| + | |||
| + | 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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| + | Anyone know what format we should be putting our references in? | ||
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| + | For references, follow the format used in the example on the Asp receptor and they will be put in automatically. | ||
| + | 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). | ||
| + | <ref>PMID: 8486661</ref> | ||
| + | You also need to add the section: | ||
| + | |||
| + | '''References''' | ||
| + | <references/> | ||
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| + | Hey guys this is just a useful tip: | ||
| + | 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. | ||
| + | |||
| + | To highlight some interesting portion of your protein: | ||
| + | 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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Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley | Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley | ||
Revision as of 15:25, 17 February 2012
This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!
Spring 2012 Chem423 Team Projects: Understanding the chemical basis of disease and life processes
Follow instructions posted at Student Projects for UMass Chemistry 423 Spring 2012.
Presentation dates: Teams, Topics, and Links
Jessica Royal, Anh Huynh, Stephanie Bristol, Emily Brackett
William Yarr, Ryan Colombo, Joey Nguyen, Jacqueline Pasek-Allen
Ryan Deeney, Jeffrey Boerth, Kate Liedell, Rebecca Bishop
Julia Tomaszewski, Sam Kmail, Nicole Bundy, Jesse Guillet
Alex Gramann, William Frantz, Felix Alfonso, Paula Preap
Greg Keohane, Nicole Hofstetter, Gina Lein, Brett Clinton, Louis Pires
Polina Berdnikova, James Hamblin, Jill Carlson, Evan Donadt
Max Nowark, Kyle Reed, Kevin Dillon, Chris Carr
Di Lin, Jill Moore, Austin Virtue, Alexander Way
Questions & Answers
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.
A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).
Anyone know what format we should be putting our references in?
For references, follow the format used in the example on the Asp receptor and they will be put in automatically. 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). [1] You also need to add the section:
References
- ↑ Yeh JI, Biemann HP, Pandit J, Koshland DE, Kim SH. The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding. J Biol Chem. 1993 May 5;268(13):9787-92. PMID:8486661
Hey guys this is just a useful tip:
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.
To highlight some interesting portion of your protein: 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.
It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.
Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley
