Protein Modeling C

RishiVanga
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Re: Protein Modeling C

Postby RishiVanga » November 26th, 2018, 5:31 am

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?

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Re: Protein Modeling C

Postby MyWorldRules » November 26th, 2018, 5:49 am

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

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Re: Protein Modeling C

Postby greenMountainCoffee » November 26th, 2018, 8:04 am

Limke wrote:
greenMountainCoffee wrote: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?

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Re: Protein Modeling C

Postby meierfra » November 26th, 2018, 10:14 am

RishiVanga wrote: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/Science-Olympiad-Protein-Modeling-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/?coliid=I2156SR4Z2GC0O&colid=1IBCH6FIA9NW&psc=0&ref_=lv_ov_lig_dp_it that Andy Hamm suggested to me. (It says size 12, but you just get one 32' roll.)

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Re: Protein Modeling C

Postby pikachu4919 » November 26th, 2018, 2:55 pm

meierfra wrote:
RishiVanga wrote: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/Science-Olympiad-Protein-Modeling-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/?coliid=I2156SR4Z2GC0O&colid=1IBCH6FIA9NW&psc=0&ref_=lv_ov_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.
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Re: Protein Modeling C

Postby Limke » November 27th, 2018, 4:58 am

greenMountainCoffee wrote:
Limke wrote:
greenMountainCoffee wrote: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?


Yes.

I measured mine out to be 85 residues.
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Re: Protein Modeling C

Postby daydreamer0023 » November 27th, 2018, 8:20 am

When has/will the On-Site model protein been/be determined? Is it supposed to be the CRISPR, since we're modelling anti-CRISPR for the pre-build? I understand that the specific section won't be given until competition.
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Re: Protein Modeling C

Postby JoeyC » November 27th, 2018, 11:34 am

The onsite build can be any protein they choose. (from what I understand)
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Re: Protein Modeling C

Postby CookiePie1 » November 27th, 2018, 2:05 pm

daydreamer0023 wrote:When has/will the On-Site model protein been/be determined? Is it supposed to be the CRISPR, since we're modelling anti-CRISPR for the pre-build? I understand that the specific section won't be given until competition.


From the MSOE website, the onsite builds will be a specific section of the CRISPR Cas-9 protein from PDB File 5f9r.pdb.
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Re: Protein Modeling C

Postby greenMountainCoffee » November 27th, 2018, 5:07 pm

Limke wrote:
greenMountainCoffee wrote:
Limke wrote:
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?


Yes.

I measured mine out to be 85 residues.


Okay, yes (sorry this is taking so long to marinate in my brain) but the toober is only 168 cm long in the kit. 168/2 = 84....? So we must not include the actual residue of either 1 or 85 correct?

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Re: Protein Modeling C

Postby MacintoshJosh » November 27th, 2018, 7:39 pm

Sorry for adding another question to the mix, but when typing "restrict 1-85", 3 chains show up - A, B , and C chains. Using FASTA sequences for the 5vw1.pdb file, I've found that chain A is the match and not chain B, as the Jmol and other people have stated. Chain B actually matches the 5xn4.pdb file, which isn't the file we're building on.

I'm confused because the Jmol states that:
The 2018-19 Pre-Build Model should represent amino acids 1 - 85 of chain B of the anti-CRISPR protein based on the PDB file 5vw1.pdb.

However, chain B doesn't match the 5vw1.pdb file. Also the official rules clarification doesn't mention anything about chains so I'm a little lost and wondering if anyone can clarify how to get to the specified section of the protein and explain which chains to restrict or not.

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Re: Protein Modeling C

Postby JoeyC » November 28th, 2018, 4:25 am

restrict 1-85
restrict :b
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Re: Protein Modeling C

Postby voisinet22 » November 28th, 2018, 1:15 pm

JoeyC wrote: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/1UQgeeSXoNnIR7ZOjLpnYPizFRMJlR7bK/view?usp=sharing


I'm not sure what the chain is supposed to look like, not sure if I'm just using a different program or not using the right commands.. I did enter the restrict 1-85 and the restrict :b
https://drive.google.com/file/d/1W3N72p ... sp=sharing

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Re: Protein Modeling C

Postby daydreamer0023 » November 28th, 2018, 1:27 pm

voisinet22 wrote:
JoeyC wrote: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/1UQgeeSXoNnIR7ZOjLpnYPizFRMJlR7bK/view?usp=sharing


I'm not sure what the chain is supposed to look like, not sure if I'm just using a different program or not using the right commands.. I did enter the restrict 1-85 and the restrict :b
https://drive.google.com/file/d/1W3N72p ... sp=sharing


You probably have to use a command like:

backbone 1.5 only

to get the carbon backbone to show up in a way that you can model it. To compare to JoeyC's images use:

cartoon only
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Re: Protein Modeling C

Postby JoeyC » November 28th, 2018, 1:41 pm

Oh. using jMol the java program is usually better, but use Ribbon only then backbone 1.0
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