Protein Modeling C [NY Trial]

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AlchemyRocks
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Re: Protein Modeling C [NY Trial]

Postby AlchemyRocks » March 24th, 2010, 1:56 pm

Quick Question.

Can crosslinkers be used to show bonds other than disulfide bonds?

Because, other than the one disulfide bond in the model, we don't know what to do with the other crosslinkers...
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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » March 24th, 2010, 3:47 pm

Quick Question.

Can crosslinkers be used to show bonds other than disulfide bonds?

Because, other than the one disulfide bond in the model, we don't know what to do with the other crosslinkers...
Crosslinkers can be used to show whatever you want, as long as it's clear what they stand for. In my original model, the crosslinkers were just there to provide stability. I've since taken them all out and replaced them with wire supports. You don't even have to use them at all if you don't feel they add anything to your model.
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Re: Protein Modeling C [NY Trial]

Postby Starapollo1 » March 31st, 2010, 6:43 pm

Is anyone using materials besides the pre build stuff?
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Re: Protein Modeling C [NY Trial]

Postby kwijiborjt » March 31st, 2010, 9:37 pm

Yeah you can definitely use other materials. I think you're supposed to use the mini toobers for the backbone of the protein, but beyond that you're only limited by your own creativity!
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Re: Protein Modeling C [NY Trial]

Postby kjhsscioly » April 6th, 2010, 8:22 pm

This is also a trial in IL, which I happen to be doing

the model for state and regionals is the same, but the color of the toober is different.... do you think we have to build a new model and will the check te color of the toober?

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » April 7th, 2010, 2:43 pm

This is also a trial in IL, which I happen to be doing

the model for state and regionals is the same, but the color of the toober is different.... do you think we have to build a new model and will the check te color of the toober?
It says in the rules that you can use the same model for Regionals and States (although you're expected to add to it for States). They give out different colored toobers to different teams, anyway, so I'm pretty sure the color is irrelevant.
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Re: Protein Modeling C [NY Trial]

Postby kjhsscioly » April 7th, 2010, 4:01 pm

okay :D

also, how do you enable hydrogen bonds on JMol, because I am just not seeing any

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » April 7th, 2010, 5:05 pm

okay :D

also, how do you enable hydrogen bonds on JMol, because I am just not seeing any
I believe the command is "hbonds on".
Also, that will show hydrogen bonds going every which way- if you want them to show the connections between parts of the backbone, you need to also type "set hbonds backbone".
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Re: Protein Modeling C [NY Trial]

Postby kjhsscioly » April 7th, 2010, 5:08 pm

I tried that, but I must have been doing it wrong because I didn't see a single bond :?

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » April 8th, 2010, 11:17 am

I tried that, but I must have been doing it wrong because I didn't see a single bond :?
Make sure you have the section where you want to show the hydrogen bonds selected; if you have a single sidechain selected or something, nothing will show up. That's the only thing I can think of. Other than that, I don't know what the problem could be :-P
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