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Re: Protein Modeling C

Posted: November 27th, 2018, 4:58 am
by 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.
Right but then... the protein would be 85 residues right?
Yes.

I measured mine out to be 85 residues.

Re: Protein Modeling C

Posted: November 27th, 2018, 8:20 am
by daydreamer0023
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.

Re: Protein Modeling C

Posted: November 27th, 2018, 11:34 am
by JoeyC
The onsite build can be any protein they choose. (from what I understand)

Re: Protein Modeling C

Posted: November 27th, 2018, 2:05 pm
by CookiePie1
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.

Re: Protein Modeling C

Posted: November 27th, 2018, 5:07 pm
by greenMountainCoffee

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?

Re: Protein Modeling C

Posted: November 27th, 2018, 7:39 pm
by MacintoshJosh
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.

Re: Protein Modeling C

Posted: November 28th, 2018, 4:25 am
by JoeyC
restrict 1-85
restrict :b

Re: Protein Modeling C

Posted: November 28th, 2018, 1:15 pm
by voisinet22
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

Re: Protein Modeling C

Posted: November 28th, 2018, 1:27 pm
by daydreamer0023
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

Re: Protein Modeling C

Posted: November 28th, 2018, 1:41 pm
by JoeyC
Oh. using jMol the java program is usually better, but use Ribbon only then backbone 1.0