Protein Modeling C

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Limke
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Re: Protein Modeling C

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

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

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


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

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
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

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
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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