Protein Modeling C

[ericlepanda]

Wait how do we figure out the amino acid sequence of the Anti-Crispr

you can find the sequences for both the anti-crispr and the cas-9 on rcsb
http://www.rcsb.org/pdb/explore/remedia ... ureId=5VW1

[PeptoBismol]

With 5vw1, I restricted it to the b chain only and found that, when I restricted it to 1-60 through 1-85 nothing happened, but when I restricted it to 1-59, some of the chain was removed, which makes me believe the b chain is 60 residues long. But I know it is at least 85 long, so how does this work out? Am I doing something wrong, or does the build contain both a and b?

[JoeyC]

restrict 1-85
restrict :b
If the chain does not have 3 Alpha Helices and 3 Beta Pleated Sheets, your program is recognizing the wrong chain.
It should look as such: https://drive.google.com/file/d/1UQgeeS ... sp=sharing

[greenMountainCoffee]

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too

[Limke]

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too

Yes, include residue 1 and 85*.
Also, just a clarification, the rules say to build residues 1-85.

[RishiVanga]

So I don't know if I'm just searching it wrong but I can't seem to find a place to buy Mini Toobers for modeling the structure. Could someone send me a link to where I can buy them?

[MyWorldRules]

Can someone please send us their files containing their work. I am really confused and would like to reference of someone. Thx x

[greenMountainCoffee]

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too

Yes, include residue 1 and 85*.
Also, just a clarification, the rules say to build residues 1-85.

Right but then... the protein would be 85 residues right?

[meierfra]

So I don't know if I'm just searching it wrong but I can't seem to find a place to buy Mini Toobers for modeling the structure. Could someone send me a link to where I can buy them?

This https://www.3dmoleculardesigns.com/Scie ... g-Kits.htm is the site to buy a Mini Toober for the Pre-Build. You can also buy a practice kit that was the 2016 Regional On-site. This is the information page; click the blue "Buy Now" button to take you to a shopping page.

You know you don't have to buy the Mini Toobers. Less expensive options include 12 guage wire and this foam wire https://www.amazon.com/dp/B0026WGDYW/?c ... _lig_dp_it that Andy Hamm suggested to me. (It says size 12, but you just get one 32' roll.)

[pikachu4919]

So I don't know if I'm just searching it wrong but I can't seem to find a place to buy Mini Toobers for modeling the structure. Could someone send me a link to where I can buy them?

This https://www.3dmoleculardesigns.com/Scie ... g-Kits.htm is the site to buy a Mini Toober for the Pre-Build. You can also buy a practice kit that was the 2016 Regional On-site. This is the information page; click the blue "Buy Now" button to take you to a shopping page.

You know you don't have to buy the Mini Toobers. Less expensive options include 12 guage wire and this foam wire https://www.amazon.com/dp/B0026WGDYW/?c ... _lig_dp_it that Andy Hamm suggested to me. (It says size 12, but you just get one 32' roll.)

I would say that from an objective standpoint, the main advantage with buying the kits to build with would be that everything is cut to the exact length that the model needs to be, as well as the fact that it provides some supports and caps for the N and C termini, and the onsite practice kits also have model amino acid parts as well (although that's not necessarily the most efficient way to get amino acid residues, you can easily make them out of whatever material your heart desires within the scope of the rules).

It's more or less a convenience thing, if anything. I know plenty of models have been really good and high-scoring without using the kits as well. Totally up to you.