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Re: Protein Modeling C

Posted: January 19th, 2019, 10:16 am
by CookiePie1
Does anyone know if for the competition they use the in-browser Jmol or the program?
In the past they have used the in-browser Jmol.
From the CBM website, it seems that the Jmol program is a last-resort for people who can't use the internet at their competitions. I think it would be a good idea to get farmiliar with both, in case you do have to use the program. They're both pretty simple and similar though, so you shouldn't have too much of a problem.

Re: Protein Modeling C

Posted: January 20th, 2019, 10:29 am
by eagerlearner102
For those that did this event in the past, do you have any idea of how many nucleotides long is the on build model? I am researching the 5f9r protein that is going to be the on build protein and on ebi.ac.uk I found some side chain to be around 30 nucleotides long.
https://www.ebi.ac.uk/pdbe/entry/pdb/5f9r/analysis

Re: Protein Modeling C

Posted: January 20th, 2019, 2:44 pm
by CookiePie1
For those that did this event in the past, do you have any idea of how many nucleotides long is the on build model? I am researching the 5f9r protein that is going to be the on build protein and on ebi.ac.uk I found some side chain to be around 30 nucleotides long.
https://www.ebi.ac.uk/pdbe/entry/pdb/5f9r/analysis
I'm not quite sure what you mean, but the onsite builds are protein chains within the regular CRISPR protein. You won't have to model any DNA. You're also not supposed to know which chains you are building onsite, so I wouldn't worry about that too much.

Re: Protein Modeling C

Posted: January 20th, 2019, 6:56 pm
by primitivepolonium
For those that did this event in the past, do you have any idea of how many nucleotides long is the on build model? I am researching the 5f9r protein that is going to be the on build protein and on ebi.ac.uk I found some side chain to be around 30 nucleotides long.
https://www.ebi.ac.uk/pdbe/entry/pdb/5f9r/analysis
The onsite build will be different for every competition. You'll show up to testing, be presented with a precut toober and some amino acids, and have to build it on the spot with the help of jmol, a ruler, and a sharpie (the latter two you should bring). It'll all be protein; no DNA (although DNA is certainly within the scope of the written exam if it's an important strand).

As for length: competitions testing at the Regionals and Invitational difficulties will have onsites of ~20-30 residues. By Nationals, onsite lengths will reach up to 90. States, I surmise, will have a length in between.

Re: Protein Modeling C

Posted: January 21st, 2019, 4:17 pm
by greenMountainCoffee

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?
You absolutely need to include 1 and 85. Make sure the Toober is completely unwound. Sometimes if if's twisted a little, that will take up some length. Pull it all the way out, so you're sure it's at its maximum length. If it's still only 168cm, you should contact the MSOE people and ask for a replacement.

EDIT: Oops. They are sending you 168 cm and CBM gives a good explanation of why they only give you 168 cm on their Ask the CBM, question 52. https://cbm.msoe.edu/scienceOlympiad/participant2.php
Gotcha thanks!

Re: Protein Modeling C

Posted: January 26th, 2019, 5:35 pm
by 'JordanC22
How should I go about labeling my protein? I am totally new to this event. Any insight would be much appreciated.

Re: Protein Modeling C

Posted: January 27th, 2019, 4:38 pm
by CookiePie1
How should I go about labeling my protein? I am totally new to this event. Any insight would be much appreciated.
What do you mean by labeling your protein?

Re: Protein Modeling C

Posted: January 29th, 2019, 11:52 am
by highbuilder
what should be on my cheat sheet. I was thinking of maybe putting jmol commands, as well as information regarding the written test, any advice on what I should put on my cheat sheet?

Re: Protein Modeling C

Posted: January 29th, 2019, 11:55 am
by highbuilder
How should I go about labeling my protein? I am totally new to this event. Any insight would be much appreciated.
What do you mean by labeling your protein?
I think they mean how to label/differentiate add-ons such as sidechains, DNA, molecules, etc.

Re: Protein Modeling C

Posted: January 29th, 2019, 12:08 pm
by highbuilder
can anyone send me a picture of their pre-model, or recommend which add-ons to add. If not, can you at least direct me to a source or guide me to where I can learn more about which add-ons are important. I was put into this event just 4 days before my comp, so I really need help :D. Thanks!