Protein Modeling C

Re: Protein Modeling C

Postby EastStroudsburg13 on Tue Oct 04, 2011 11:11 am

TheGenius wrote:
EASTstroudsburg13 wrote: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 "Website restore error". Anyone else experiencing this or is it just me? :?

You need Java if you don't have it installed. If you're using IE, try compatibility view.

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 on Tue Oct 04, 2011 7:05 pm

amerikestrel wrote: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 on Wed Oct 05, 2011 11:36 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 on Wed Oct 05, 2011 5:26 pm

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

Postby Phenylethylamine on Thu Oct 06, 2011 5:52 pm

EASTstroudsburg13 wrote: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.
TheGenius wrote: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 on Sat Oct 08, 2011 2:51 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.
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Re: Protein Modeling C

Postby amerikestrel on Sat Oct 08, 2011 4:27 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 on Sat Oct 08, 2011 8:42 pm

amerikestrel wrote: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.
amerikestrel wrote: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 on Sat Oct 08, 2011 8:58 pm

Thanks!
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Re: Protein Modeling C

Postby bocahighscienceolypm on Thu Oct 20, 2011 4:20 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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Re: Protein Modeling C

Postby XXGeneration on Thu Oct 20, 2011 4:35 pm

Correct me if I'm wrong, but isn't the Chain A supposed to be 298 cm? It's 2 cm per amino acid and I read that it was 149 amino acids.
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Re: Protein Modeling C

Postby Phenylethylamine on Thu Oct 20, 2011 5:19 pm

bocahighscienceolypm wrote: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?
XXGeneration wrote:Correct me if I'm wrong, but isn't the Chain A supposed to be 298 cm? It's 2 cm per amino acid and I read that it was 149 amino acids.

Although the first residue of chain A is 148 and the last is 296, the chain is only 143 amino acids in length– as the prebuild kit page explains, the numbering is not consecutive:
Please Note!

The numbering in the PDB file 1i3o is not consecutive. In the field of caspase research, scientists number caspase proteins based on the numbering of caspase-1. Researchers can then compared the sequences between the members of the caspase family to look for insertions/deletions.
They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.
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Re: Protein Modeling C

Postby XXGeneration on Fri Oct 21, 2011 7:45 pm

Thank you for the clarification; the link will be very helpful in numbering the toober hehe :3
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Re: Protein Modeling C

Postby kwijiborjt on Sun Oct 23, 2011 5:07 pm

starpug wrote:Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?


Winning teams usually have taken some effort to display their protein. I can give some examples from last year's NY competition to illustrate what is useful:

One team built a large sideless cube with a poster on the back with beautiful elaborate drawings. While they clearly put a lot of effort in, i couldn't give them creative addition points for their drawings because they had little to nothing to do with the relationship between the structure and function of Klf4.

My high school team used to use a very un-elaborate ring stand (think chemistry) as structural support and would clamp the protein to hold it in place. The ringstand was mounted on a painted wooden board which could be used to display extra items for creative additions as well as the note card.

Many teams make some sort of frame out of balsa wood or another material so that they have something to hang their protein from.

It's useful to have something to keep your protein fixed so that it won't get bent out of shape in transit or from you or the judges handling it. It also adds to the presentation value. While you don't get points specifically for presentation value, an attractive (=/= elaborate) display can positively influence the judges in their somewhat subjective evaluation process.
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Re: Protein Modeling C

Postby bocahighscienceolypm on Tue Oct 25, 2011 4:26 pm

They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.


Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?
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