Protein Modeling C

Locked
User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by Phenylethylamine »

bocahighscienceolypm wrote:
They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.
Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?
How are you finding that they "do not exist"? When I look at the pdb file, they are there.

Try opening the PDB in Jmol (or going to the online prebuild environment, I don't know what you prefer to use) and, before typing anything else, type "restrict *b and 310-401". Chain B – amino acids 310 through 401 – should appear.

If this doesn't work, there are a couple possibilities I've thought of: if you're using standalone Jmol on your computer and have downloaded the PDB file, I suppose it is possible that your download was cut short and you're missing part of the file... in which case you could try re-downloading the file. If you're using the online environment or are using standalone Jmol but are certain that all your downloads were complete, my best guess is that you used a command that caused chain B to be excluded (e.g., "restrict *a") and then afterwards tried to look at chain B. Try "select all", then "backbone" (or any other viewing command, just to get everything visible again), and then "restrict *b and 310-401".
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
bocahighscienceolypm
Member
Member
Posts: 3
Joined: October 20th, 2011, 1:14 pm
Division: C
State: FL
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by bocahighscienceolypm »

Phenylethylamine wrote:
bocahighscienceolypm wrote:
They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.
Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?
How are you finding that they "do not exist"? When I look at the pdb file, they are there.

Try opening the PDB in Jmol (or going to the online prebuild environment, I don't know what you prefer to use) and, before typing anything else, type "restrict *b and 310-401". Chain B – amino acids 310 through 401 – should appear.

If this doesn't work, there are a couple possibilities I've thought of: if you're using standalone Jmol on your computer and have downloaded the PDB file, I suppose it is possible that your download was cut short and you're missing part of the file... in which case you could try re-downloading the file. If you're using the online environment or are using standalone Jmol but are certain that all your downloads were complete, my best guess is that you used a command that caused chain B to be excluded (e.g., "restrict *a") and then afterwards tried to look at chain B. Try "select all", then "backbone" (or any other viewing command, just to get everything visible again), and then "restrict *b and 310-401".
It was something odd with the commands we were using, thanks for the advice.
User avatar
akatsuki9
Member
Member
Posts: 17
Joined: November 10th, 2011, 12:31 pm
Division: C
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by akatsuki9 »

Hey,

At my first invitational, they gave us pipe cleaners for the on-site model. Will they give us a minitoober(s) for district? The pipe cleaners aren't that great for a protein model because they don't keep their shape as well.
Also, are there any good textbooks out there to study from for this event?
Quoth the raven... "NEVERMORE"
User avatar
Lily Essence
Member
Member
Posts: 67
Joined: March 29th, 2009, 1:36 pm
Division: C
State: TX
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by Lily Essence »

I know this thread is not the place to complain about an event, but I am deeply disappointed in the amount of on-site builds this year (yet again).

Last year, as the first year this event came out, the only times I ever got to model were for state (nervous as heck since it was my first onsite build... AT STATE), and nationals, despite also going to regionals and two invitationals. The kits for the onsite builds were purchasable from the website. I passed this off as an unforeseen complication since the event was new, and asked the proctors at nationals about it. On the sheet asking about my experience, I commented on how there just wasn't enough onsite building experience available, whether the problem be price or something else.

This year, the kits are being sold at cost, and sadly both of the invitationals that my team is going to isn't offering a true "on-site build". One offered pipecleaners and an extremely simple protien, the other is telling competitors that there will be no onsite build a head of time. Hopefully, my regionals will offer a proper onsite build, but honestly, this isn't the way to run such a planned event.

What are you guys' experience with the whole on-site build portion of the exam? Is it really necessary to have 3 people for just a onsite test?
Silent and Listen are spelled with the same letters
Seven Lakes SLHS Science Olympiad
Retiring my competition career! Off to scold the newbies as a manager!
User avatar
akatsuki9
Member
Member
Posts: 17
Joined: November 10th, 2011, 12:31 pm
Division: C
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by akatsuki9 »

Lily Essence wrote:I know this thread is not the place to complain about an event, but I am deeply disappointed in the amount of on-site builds this year (yet again).

Last year, as the first year this event came out, the only times I ever got to model were for state (nervous as heck since it was my first onsite build... AT STATE), and nationals, despite also going to regionals and two invitationals. The kits for the onsite builds were purchasable from the website. I passed this off as an unforeseen complication since the event was new, and asked the proctors at nationals about it. On the sheet asking about my experience, I commented on how there just wasn't enough onsite building experience available, whether the problem be price or something else.

This year, the kits are being sold at cost, and sadly both of the invitationals that my team is going to isn't offering a true "on-site build". One offered pipecleaners and an extremely simple protien, the other is telling competitors that there will be no onsite build a head of time. Hopefully, my regionals will offer a proper onsite build, but honestly, this isn't the way to run such a planned event.

What are you guys' experience with the whole on-site build portion of the exam? Is it really necessary to have 3 people for just a onsite test?
See my above post.
Quoth the raven... "NEVERMORE"
User avatar
EastStroudsburg13
Admin Emeritus
Admin Emeritus
Posts: 3203
Joined: January 17th, 2009, 7:32 am
Division: Grad
State: PA
Pronouns: He/Him/His
Has thanked: 48 times
Been thanked: 204 times
Contact:

Re: Protein Modeling C

Post by EastStroudsburg13 »

Well, this is one reason the on-site build is only 30% of the event.

At regionals, they will almost certainly have actual Toobers for modeling. If they don't, well, then there's something wrong, since it's not like an invite, which is just practice. The major invites like Solon and Mentor will also probably have Toobers, but some of the less commonly-attended ones might not, and you'll have to deal with that. It actually might be good practice to have to deal with something that doesn't hold its shape as well.

I think it is necessary to have 3. You have to deal with both the test and the model at the same time, and in order to model the protein quickly, sometimes you have to have 2 people working together. Then, the third person can work on the test, and if there's time, the you can go over the test together and tweak your model. I think, with only 2 people, they would both have to be very strong (and be able to work independently) in the event, otherwise you may run out of time trying to focus on one part and not the other.

I don't know about textbooks personally. Phenyl might have suggestions, but I'd just say that an AP Bio book might be helpful with regards to general protein information. Other than that, the Internet is your friend. :)
East Stroudsburg South Class of 2012, Alumnus of JT Lambert, Drexel University Class of 2017

Helpful Links
Wiki
Wiki Pages that Need Work
FAQ and SciOly FAQ Wiki
Chat (See IRC Wiki for more info)
BBCode Wiki


So long, and thanks for all the Future Dictator titles!
User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by Phenylethylamine »

EASTstroudsburg13 wrote:I think it is necessary to have 3. You have to deal with both the test and the model at the same time, and in order to model the protein quickly, sometimes you have to have 2 people working together. Then, the third person can work on the test, and if there's time, the you can go over the test together and tweak your model. I think, with only 2 people, they would both have to be very strong (and be able to work independently) in the event, otherwise you may run out of time trying to focus on one part and not the other.
The NY State people have already stated that teams will only get two students on the event at States. Personally, I think that should be fine – I did the event as a trial two years ago, when it was only two people, anyway. Have one person put together the onsite, the other work on the test, and then when the onsite is finished, switch – the other person can check over the onsite, and the one who did the onsite can fill in anything on the test that the first person didn't get.
EASTstroudsburg13 wrote:I don't know about textbooks personally. Phenyl might have suggestions, but I'd just say that an AP Bio book might be helpful with regards to general protein information. Other than that, the Internet is your friend. :)
For the specifics of the prebuild and onsite, I'd recommend reading the PDB primary citation, as well as searching the PDB ID on Google Scholar to find other papers about the protein. They can be a little dense, but that's the best way to find out what residues are important to the protein's function, and in what way. Also, get familiar with Jmol, and use it to look at the protein until you know the structure backwards and forwards (if you download standalone Jmol, you can look at the onsite in advance, too).

Sorry, I can't recommend any textbooks; I don't use them, myself. The Internet, as EASTstroudsburg said, is your friend.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
XXGeneration
Member
Member
Posts: 96
Joined: February 23rd, 2011, 4:39 pm
Division: C
State: NJ
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by XXGeneration »

Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?
User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by Phenylethylamine »

XXGeneration wrote:Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?
Sadly, I haven't gotten that far yet. Get back to me in about a month, when Intel submission has passed and I'm between waves of college apps >.<
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
XXGeneration
Member
Member
Posts: 96
Joined: February 23rd, 2011, 4:39 pm
Division: C
State: NJ
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by XXGeneration »

Phenylethylamine wrote:
XXGeneration wrote:Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?
Sadly, I haven't gotten that far yet. Get back to me in about a month, when Intel submission has passed and I'm between waves of college apps >.<
T-T

Is there any good number for creative additions?
Locked

Return to “2012 Lab Events”

Who is online

Users browsing this forum: No registered users and 3 guests