Protein Modeling C

[The Eviscerator]

Thanks.

Also, which cap (blue or red) is the n-terminus and which cap is the c-terminus?
And, just for clarification since I'm paranoid, the n-terminus is at the beginning of the polypeptide, correct?

[FullMetalMaple]

I'm trying to model DNA as a creative addition right now. I have an extra toober (too short, from last year) that I want to use as the 2 sugar-phosphate backbones of the DNA. Would this be okay, or are the toobers only allowed to be used for protein backbones?

I don't think there's anything that says you can't use toobers for other parts of your model; however, make sure that your key makes it clear what's part of the protein and what's part of the DNA.

To add to that, I think it would be especially helpful if the toober you use for the DNA is a different color.

Thanks.

Also, which cap (blue or red) is the n-terminus and which cap is the c-terminus?
And, just for clarification since I'm paranoid, the n-terminus is at the beginning of the polypeptide, correct?

I'm pretty certain blue is the n-terminus and red the c-terminus. And yes, the n-terminus is at the beginning.

[AlphaTauri]

Type "color group" into Jmol (make sure you have the protein selected) and it should show you the n- and c- terminuses (termini?). They're even color-coded nicely.

[The Eviscerator]

Type "color group" into Jmol (make sure you have the protein selected) and it should show you the n- and c- terminuses (termini?). They're even color-coded nicely.

So once that's done, the blue side (first couple residues) is the N-terminus and is where the blue cap goes, and the red side (last couple residues) is the C-terminus and is where the red cap goes?

[AlphaTauri]

Yep, it's that simple!

Although on proteins where you don't have the n- or c- terminus shown as part of the file, just go by which end is "closer" to red/blue (i.e. if one end is orange and the other is green, put the red cap where the orange end is and the blue where the green is).

[The Eviscerator]

Great! I learned something today and it's saturday.
I'm having trouble getting the zinc atoms and hydrogen bonds to show up on the online jmol prebuild environment though... Can someone help me?

[Infinity Flat]

Great! I learned something today and it's saturday.
I'm having trouble getting the zinc atoms and hydrogen bonds to show up on the online jmol prebuild environment though... Can someone help me?

Usually I just go:
Right Click -> Select -> Element -> Zinc
to select the zinc
and then use the style menu to toy with its appearance.

EDIT:
Just toying around, I found
Right Click -> Style -> H-Bond -> Calculate shows the H-bonds for the a-helices, B-sheets, and within the DNA

[The Eviscerator]

Great! I learned something today and it's saturday.
I'm having trouble getting the zinc atoms and hydrogen bonds to show up on the online jmol prebuild environment though... Can someone help me?

Usually I just go:
Right Click -> Select -> Element -> Zinc
to select the zinc
and then use the style menu to toy with its appearance.

EDIT:
Just toying around, I found
Right Click -> Style -> H-Bond -> Calculate shows the H-bonds for the a-helices, B-sheets, and within the DNA

The zinc ion thing worked, but the hydrogen bonds won't show up. What are the hydrogen bonds supposed to look like if they show up? I haven't gotten it to work yet, but I'm expecting dotted lines...

[TheGenius]

There is probably a better way, but try typing into the console, "calculate hbonds". If I remember correctly, that should show the hydrogen bonds as dashed lines.

[The Eviscerator]

There is probably a better way, but try typing into the console, "calculate hbonds". If I remember correctly, that should show the hydrogen bonds as dashed lines.

Thanks, it worked. So how do you make disulfide bonds show up and the other types of bonds?
And what is hetero?

Also, does the prebuild (klf4) have 2 zinc fingers or 3? There are 3 zinc atoms, but the last third of the protein has a shorter alpha helix and loop than the other 2 zinc fingers, making me think that it isn't a zinc finger.