Protein Modeling C

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EastStroudsburg13
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Re: Protein Modeling C

Postby EastStroudsburg13 » October 4th, 2011, 8:11 am

I decided recently to look at the jmol for this year, and I can't view it on my computer. Whenever I try to view it, it comes up with a [url=res://ieframe.dll/acr_error.htm#msoe.edu,http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html]"Website restore error"[/url]. Anyone else experiencing this or is it just me? :?
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Okay, that might be it. I definitely didn't use IE 9 last year for PM. If all else fails, I guess I can just use Firefox.
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Re: Protein Modeling C

Postby Phenylethylamine » October 4th, 2011, 4:05 pm

What are the advantages of using the standalone Jmol application instead of the web applet?
For one, it allows you to practice with the on-site build proteins before the competition. With the webapp, you can only look at the pre-loaded prebuild protein.

Also, the webapp is an incredible pain to use- you have to click "execute" manually every time you want to execute a command, and you have to delete the previous command in order to type in a new one, as the previous command isn't automatically removed when you execute it. It seems quite poorly designed to me, and using it in competition is always tremendously frustrating for me (I suppose I could practice with it out of competition until it bothered me less, but it's just so... unpleasant xP).
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Re: Protein Modeling C

Postby EastStroudsburg13 » October 5th, 2011, 8:36 am

Wait, so you can get Jmol on your computer and then use it to model the proteins, without using the link they give us? f that's so, I want it, it could make everything much easier. :mrgreen: I'm guessing you can't use it on competition day.
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Re: Protein Modeling C

Postby TheGenius » October 5th, 2011, 2:26 pm

Jmol.
Sometimes event supervisors use the standalone application.
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Re: Protein Modeling C

Postby Phenylethylamine » October 6th, 2011, 2:52 pm

Wait, so you can get Jmol on your computer and then use it to model the proteins, without using the link they give us? f that's so, I want it, it could make everything much easier. :mrgreen: I'm guessing you can't use it on competition day.
There's an explanation of how to download it on the Protein Modeling Wiki.
Jmol.
Sometimes event supervisors use the standalone application.
Sometimes they do, but it unfortunately doesn't seem to be very common.

At the Eastern Long Island Regionals, they give you the choice of using the online environment or standalone RasMol, which is slightly different from Jmol. Fortunately, I actually learned to use RasMol before I'd even heard of Jmol, so that works perfectly for me, but anyone who hasn't used RasMol is stuck with the choice of dealing with the annoying online environment, or trying to guess what the RasMol command they want is every time there's a difference from Jmol (there aren't that many differences, but there are a few key ones that I can't think of at the moment).
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Re: Protein Modeling C

Postby amerikestrel » October 8th, 2011, 11:51 am

In Jmol, I know that there's backbone, wireframe, and spacefill modes, but the proteins look different when you first open a file (like the pictures here). What is this called?

Also, which display mode is the best to use when modeling the protein?

EDIT: just read that the model must be based off the "alpha carbon backbone display", so I guess that answers my second question.
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Re: Protein Modeling C

Postby amerikestrel » October 8th, 2011, 1:27 pm

New question: what are the crosslinkers that came in the prebuild kit for? I don't find any mention of them in the wiki or the MSOE videos.
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Re: Protein Modeling C

Postby Phenylethylamine » October 8th, 2011, 5:42 pm

In Jmol, I know that there's backbone, wireframe, and spacefill modes, but the proteins look different when you first open a file (like the pictures here). What is this called?

Also, which display mode is the best to use when modeling the protein?

EDIT: just read that the model must be based off the "alpha carbon backbone display", so I guess that answers my second question.
That's the "ribbon" display mode (or something like that, I've used it in other protein visualization software but since I only use Jmol for SciO, it's not the most useful mode for me in Jmol). It shows secondary structure- alpha-helices as, well, helices, and beta-sheets with arrows.

This information is on the Protein Modeling Wiki, but you should use backbone for the whole thing (as per the rules), probably wireframe for any sidechains you choose to show, and spacefill for ions.
New question: what are the crosslinkers that came in the prebuild kit for? I don't find any mention of them in the wiki or the MSOE videos.
The crosslinkers are just for increasing the structural stability of your model. They don't represent any particular structure, although I suppose you could use them to represent disulfide bonds or something similar. They end up being a few Angstroms long to scale, so it's within the plausible range for such a bond. But again, they don't represent anything unless you say they do on your card.
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Re: Protein Modeling C

Postby amerikestrel » October 8th, 2011, 5:58 pm

Thanks!
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Re: Protein Modeling C

Postby bocahighscienceolypm » October 20th, 2011, 1:20 pm

We started modeling with the longest chain, a and ran out of tuber, even with the 286 cm length...has anyone else had this problem?


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