Protein Modeling C

User avatar
kalithepianist
Member
Member
Posts: 31
Joined: December 30th, 2010, 10:00 am
Division: C
State: AZ
Location: That one place.

Re: Protein Modeling C

Postby kalithepianist » January 3rd, 2012, 7:07 pm

Has anyone happened to submit a clarification yet?
derp

User avatar
EastStroudsburg13
Administrator
Administrator
Posts: 3035
Joined: January 17th, 2009, 7:32 am
Division: Grad
State: MD
Location: At work trying to be a real adult
Contact:

Re: Protein Modeling C

Postby EastStroudsburg13 » January 4th, 2012, 8:13 am

I submitted one. I simplified the question to only refer to the Jmol, and then in additional comments I made further explanation with the PDB. I though a simplified question would work better for supervisors who might be unaware of the mistake and/or were thrown in to supervising and were not very experienced.
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
Dragonshark
Member
Member
Posts: 68
Joined: January 4th, 2012, 9:02 pm
Division: Grad
State: WI
Location: West Allis, WI

Re: Protein Modeling C

Postby Dragonshark » January 4th, 2012, 9:26 pm

I apologize if this question has already been asked before, but does anyone know what the approximate diameter of an alpha helix on a model (made from the Toobers) should be?
Nathan Hale HS SciO
2011 - Regionals/States: Anat/Phys [1/1!!!], Chem Lab [1/2]
2012 - Regionals/States: Chem Lab [1/6 >_< ], Forensics [2/1!!!], Protein [1/2], Team [9]
2013 - A/P, Chem Lab, 4N6, TPS, C/A (trial)

User avatar
akatsuki9
Member
Member
Posts: 17
Joined: November 10th, 2011, 12:31 pm
Division: C

Re: Protein Modeling C

Postby akatsuki9 » January 5th, 2012, 12:31 pm

I just wound it around my finger and adjusted it so the helix started and ended at the appropriate amino acids...
Quoth the raven... "NEVERMORE"

paradoxgirl
Member
Member
Posts: 67
Joined: December 20th, 2008, 1:35 pm
Division: Grad
State: PA

Re: Protein Modeling C

Postby paradoxgirl » January 6th, 2012, 12:33 pm

Just a thought, must creative additions be attached to the model? At some competitions last year, teams came with text on their models giving more information than their notecards stated. At one competition, a team came with a tri-fold board covered in diagrams and text.
Harriton High School Science Olympiad

Diana
Member
Member
Posts: 2
Joined: March 28th, 2011, 12:49 pm
Division: B
State: NY

Re: Protein Modeling C

Postby Diana » January 6th, 2012, 12:51 pm

Does anyone have a 2012 Protien test?
98% of scioly members have a signature, copy and paste this if you are part of the 2% who... wait... never mind.

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » January 6th, 2012, 4:44 pm

Just a thought, must creative additions be attached to the model? At some competitions last year, teams came with text on their models giving more information than their notecards stated. At one competition, a team came with a tri-fold board covered in diagrams and text.
It depends on the supervisor, but I believe that most event supervisors want creative additions to the model itself, rather than additional text explaining it. I would stay away from extra text, personally. The idea is to build a model that tells the protein's "molecular story", and it should speak for itself, with just the notecard by way of explanation.

I actually did use a text-based addition at Nationals last year, and I don't know whether or not it got me any points. But it's not really in the spirit of the prebuild, and I won't be doing that this year. It was a pretty last-minute thing, when we couldn't think of another good addition (although I wish I'd thought of adding a nucleosome; ah well). You should be able to see my model from last year (including this text thing) on the image gallery pretty soon, but I don't really recommend emulating that part of it at least.
Does anyone have a 2012 Protien test?
Probably not. It might be possible to find an unofficial one from an invitational or something, but I'm fairly sure that no official MSOE tests are released until the end of the competition season.
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

gigaboo
Member
Member
Posts: 64
Joined: February 23rd, 2011, 9:46 pm
Division: C
State: UT

Re: Protein Modeling C

Postby gigaboo » January 7th, 2012, 1:36 pm

I know that this is probably a completely stupid question, but what are the structures from 221-225 and 270-274 in Chain A and from 314-318 in Chain B? The sequence structure shows them as helices, but they don't quite line up with the amino acids that Jmol displays. And if they are non-alpha helices, then how are they folded? Sorry again from the stupid post.

ghazaly
Member
Member
Posts: 2
Joined: January 7th, 2012, 9:03 am
Division: C
State: NJ

Re: Protein Modeling C

Postby ghazaly » January 7th, 2012, 4:44 pm

hey all!
when folding the pre build model, we notice chain b is supposed to start at 310, but the jmol begins at 320...is there something wrong with out jmol, or is there something wrong with the protien labeling diagram? has anyone had this problem? we just noticed this discrepancy and dont know how to fix it, any help is greatly appreciated
thanks!

AlphaTauri
Staff Emeritus
Staff Emeritus
Posts: 829
Joined: September 11th, 2009, 1:41 pm
Division: Grad
State: PA
Location: 04h 35m 55.239s, +16° 30′ 33.49″
Contact:

Re: Protein Modeling C

Postby AlphaTauri » January 7th, 2012, 5:05 pm

You are using the 1i3o file from PDB, right? Unless there's something really screwy with Jmol, it should start at 310. If "restrict *b" doesn't work, you can always try "restrict 310-401".
Hershey Science Olympiad 2009 - 2014
Volunteer for Michigan SO 2015 - 2018

]\/[ Go Blue!


Return to “2012 Lab Events”

Who is online

Users browsing this forum: No registered users and 1 guest