Protein Modeling C

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Fluorine
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Re: Protein Modeling C

Postby Fluorine » December 18th, 2015, 6:21 pm

How do you find the range of secondary structures in Jmol? Like this sheet is from this amino acid to this amino acid this?
You can use two ways (sort of):

1) Find the sequence sheet from the protein database and look at when the secondary structure end and start

2) Color secondary structures on Jmol and then hover your mouse over where the structure starts. Eventually a white box should appear and it will tell you the number sequence. You then do the same for end too.

Just to note you have to use method 2 during the onsite build because you cannot look up the sequence sheet. If you need anything else PM me.
Alumni of FAUHS SO | Logistics Direcotor @ Cornell Scioly
Wind Power, Anatomy, Invasive Species, Materials Science, Optics, Entomology,
 Cell Biology, Fossils, Experimental Design, Protein Modeling

kwalk2016
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Re: Protein Modeling C

Postby kwalk2016 » December 19th, 2015, 7:03 am

Hi I was wondering if anyone knew how to figure out which sidechains are important to the structure and function of our model, I'm having a difficult time with that. If anyone knows could you please help me out? Thanks very much!

harik2000
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Re: Protein Modeling C

Postby harik2000 » January 3rd, 2016, 9:23 am

Hi guys, I am relatively new to this event. I have heard from my previous teamates that the onsite model will contain some aminio acids such as Hystine, Cyestine, Proline, Valine, etc. How do you calculate the exact position of those amino acids and where it should go on the toober. Is there a command that you put in the Jmol console? Thanks a lot!

Showow
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Re: Protein Modeling C

Postby Showow » January 3rd, 2016, 11:57 am

Has anyone gone to an invitational yet and got feedback on their pre-build protein model?
2015-2016 Events Clio/Eastside/Regionals/States
Experimental Design 2/6/5/20
Game On 1/11/1/10
It's About Time 4/11/2/19
Protein Modeling 2/8/1/18
Source Code (Michigan Trial Event) -/-/4/4

RAHSAndrew17
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Re: Protein Modeling C

Postby RAHSAndrew17 » January 10th, 2016, 1:45 pm

Is anyone else having trouble building the Pre-Build model for Protein Modeling due to the Toober being the incorrect length?

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Fluorine
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Re: Protein Modeling C

Postby Fluorine » January 10th, 2016, 4:56 pm

Is anyone else having trouble building the Pre-Build model for Protein Modeling due to the Toober being the incorrect length?
If you ordered the pre-build toober for this year then the length should be fine. However, if you are trying to model more than the squence set by CBM or use a toober from a previous year then that would be another story.
Alumni of FAUHS SO | Logistics Direcotor @ Cornell Scioly
Wind Power, Anatomy, Invasive Species, Materials Science, Optics, Entomology,
 Cell Biology, Fossils, Experimental Design, Protein Modeling

Showow
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Re: Protein Modeling C

Postby Showow » January 15th, 2016, 8:42 am

In previous years I know that for the explanation of creative additions was limited to a 3" x 5" index card as stated in the rules. But this year in the rules there is no specification for the size/type of paper that the creative additions are supposed to be on. (but new bolded rules give the new specifications for this year) I have submitted numerous FAQ's to have this clarified but I have gotten no responses. I just wanted to know what any of you guys were going to do for your creative addition explanations.
2015-2016 Events Clio/Eastside/Regionals/States
Experimental Design 2/6/5/20
Game On 1/11/1/10
It's About Time 4/11/2/19
Protein Modeling 2/8/1/18
Source Code (Michigan Trial Event) -/-/4/4

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Fluorine
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Re: Protein Modeling C

Postby Fluorine » January 15th, 2016, 9:00 am

In previous years I know that for the explanation of creative additions was limited to a 3" x 5" index card as stated in the rules. But this year in the rules there is no specification for the size/type of paper that the creative additions are supposed to be on. (but new bolded rules give the new specifications for this year) I have submitted numerous FAQ's to have this clarified but I have gotten no responses. I just wanted to know what any of you guys were going to do for your creative addition explanations.
I think I know what your are asking but correct me if I am wrong:

I don't know if you saw this but this might explaint it.

3.b rules says that teams should explain function of additions in 500 words or less on a 10 point single space sheet.

So as long as you additions are explained in 500 words or less I think you are good. And I mean a regular piece of printer would look fine in my opinion.
Alumni of FAUHS SO | Logistics Direcotor @ Cornell Scioly
Wind Power, Anatomy, Invasive Species, Materials Science, Optics, Entomology,
 Cell Biology, Fossils, Experimental Design, Protein Modeling

Showow
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Re: Protein Modeling C

Postby Showow » January 15th, 2016, 4:41 pm

In previous years I know that for the explanation of creative additions was limited to a 3" x 5" index card as stated in the rules. But this year in the rules there is no specification for the size/type of paper that the creative additions are supposed to be on. (but new bolded rules give the new specifications for this year) I have submitted numerous FAQ's to have this clarified but I have gotten no responses. I just wanted to know what any of you guys were going to do for your creative addition explanations.
I think I know what your are asking but correct me if I am wrong:

I don't know if you saw this but this might explaint it.

3.b rules says that teams should explain function of additions in 500 words or less on a 10 point single space sheet.

So as long as you additions are explained in 500 words or less I think you are good. And I mean a regular piece of printer would look fine in my opinion.
Yep that's what I was getting after. It's just that I have been to two workshops and both times the Protein Modeling instructors (who both happened to be actual regional supervisors) said that we needed a 3" x 5" card for the creative additions. I guess I'll probably bring in a copy of the rules and ask the supervisor(s) about their personal interpretation.
2015-2016 Events Clio/Eastside/Regionals/States
Experimental Design 2/6/5/20
Game On 1/11/1/10
It's About Time 4/11/2/19
Protein Modeling 2/8/1/18
Source Code (Michigan Trial Event) -/-/4/4

Noel
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Re: Protein Modeling C

Postby Noel » January 16th, 2016, 4:33 pm

I am assuming that since the rule writers eliminated the detail about a 3x5 notecard from last year, they no longer think it is necessary. We are only expected to comply with this year's specifications which are 500 words or less, 10 point font size, and single spaced (3.b). The supervisors you encountered probably weren't up to date with the new rules. I attended an invitational in Texas and my partners and I had no issues with our presentation, which did not include a 3x5 notecard.
2015-2016 Events
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