User talk:J. Shaun Lott

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Welcome to Proteopedia! We hope you will contribute much and well. You will probably want to read the help pages. Again, welcome and have fun! Eran Hodis 16:44, 30 May 2008 (IDT)


Your new page looks great, and I'm sure will be very helpful for your course. May I suggest something? If you notice, the "Proteopedia Page Contributors and Editors" section is right next to the 2nd applet on the page. Perhaps you'd like that section to be pushed down all the way to the bottom. Try this: insert, as the last line in the page, the text {{Clear}} (i.e. the word Clear with 2 curly brackets on either side). Save the page and you should find that the contributors section has been pushed to a more aesthetically pleasing location at the bottom of the page instead of encroaching on your 2nd applet. If you ever need to separate 2 sections, just use this clearing syntax.

Best, Eran Hodis 15:51, 15 July 2008 (IDT)

Hi Eran

Thanks for taking an interest! This is my first experiment at transferring teaching material from sPDBv to Proteopedia, and my first impression is that it will work very well, especially for courses like this: large classes, with mixed computational ability. All the time spent learning how to use the program has disappeared, and one can focus on content. The end result will be that more content goes in, which can only be good. Thanks for the formatting suggestions - I'm not done yet so I'll certainly try incorporating them. I think I still have my reservations about Jmol, which are in some degree at least down to aesthetics. For instance, can one increase the thickness rather than the width of sheets and helices so that they don't appear paper-thin? I think my wish-list from Erice is still true: would be great to have the applet launch in a stand-alone window for instance, and I find the 'control panel' window of sPDBv very useful and so something like it would be great too.

cheers J. Shaun Lott

Hi Shaun,

If you're interested in another example of teaching material on Proteopedia, there is a new (and maybe still developing) page on Ramachandran Plots that Professor Karl Oberholser from Messiah College, PA made. Here is the link: [User:Karl_Oberholser/Ramachandran_Plots] . As far as aesthetics on Jmol, does the "toggle quality" feature allay your concerns at all? I looked briefly into increasing the thickness of the sheets and helices in Jmol, but on first glance did not find this option. You are always welcome to peruse the Jmol documentation at and to recommend the inclusion of new features (although all of those powerful Jmol commands can be accessed by the Jmol command line console -- just right click on the Jmol and select console). A control panel is not a bad idea at all, but we've yet to do something like that. Again, if you have any questions just contact me.

Best, --Eran Hodis 01:31, 16 July 2008 (IDT)

P.S. I sign my name by using the signature button (2 buttons to the left of the 3D button), and if you want to leave me a note, you should do it on my user page (i.e. go to the discussion page on my user page). If you write anything there, I will be immediately notified, whereas if you write it here, I won't know unless I happen to check.

Proteopedia Page of The Year Competition

Dear Shaun,

How is your page working out for teaching? I'd love to hear your feedback, good and bad. Also, please do encourage your students to request accounts and create pages of their own -- we are hosting a Page of the Year competition with a 32GB iPod Touch as the grand prize!

With warm regards, Eran

Thanks for the comments, let me check on the points you raised and get back to you, Eran Hodis 07:40, 13 August 2008 (IDT)

Links within Proteopedia

Hi Shaun,

The usual way of creating links within Proteopedia is by surrounding the page name in square brackets like so: [[1ea5]] and if you want to specify how the text of the link should use, just use a pipe character like this [[1ea5 | this is the text that will be displayed]]. Here are the two examples: 1ea5 and this is the text that will be displayed.

External links are created using no single square brackets like so: resulting in the full link being displayed. To display only a number, use [] and do not require a pipe character to separate the link from the displayed text: [ Wikipedia!]] Now these three examples in order: and [1] and Wikipedia!

Notice that external links are differentiated from internal links via a different shade of blue and an arrow following the link indicating that the link takes you to an external website.

Best, Eran Hodis 01:08, 14 August 2008 (IDT)

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