Protein Modeling C

meierfra
Coach
Coach
Posts: 75
Joined: August 23rd, 2016, 10:01 am
Division: C
State: MI
Has thanked: 3 times
Been thanked: 11 times

Re: Protein Modeling C

Post by meierfra »

greenMountainCoffee wrote:
Limke wrote:
greenMountainCoffee wrote: 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?
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
Last edited by meierfra on January 19th, 2019, 8:07 am, edited 1 time in total.
MacintoshJosh
Member
Member
Posts: 72
Joined: October 22nd, 2017, 12:50 pm
Division: C
State: VA
Has thanked: 6 times
Been thanked: 9 times

Re: Protein Modeling C

Post by MacintoshJosh »

meierfra wrote:
greenMountainCoffee wrote:
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.
Yes, this is something extremely confusing, but do not change the length from 168cm. The MSOE site states:
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. This section is 84 amino acids long and will require a toober that is 168cm long at the scale of 1 amino acid = 2cm.
It says that the section is 84 amino acids long, which is really confusing since 1-85 is 85 amino acids long, not 84. This means that either amino acid 1 or 85 would have to be omitted to fit the 84 amino acids. For invitationals we just snipped off the last amino acid and didn't get any points off. I'm not saying you should do that either, but you need to make sure you keep the length at 168cm. Sorry if this wasn't helpful but I'm hoping someone knows a complete explanation to this.
User avatar
platypusomelette
Member
Member
Posts: 79
Joined: May 7th, 2017, 2:41 pm
Division: C
State: NY
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by platypusomelette »

Anyone know a good convenient place to learn about the amino acids in detail?
island trash trees hs
anat: reg 4th
herp: reg 6th
genes: reg 5th
protein: reg 2nd
disease: reg 15th
fossils: reg 4th
2016: a&p 1st, fossils 3rd
2017: a&p 3rd, herp 14th
2018: a&p 1st, microbe 8th, herp 13th :/
pigeon YEA WE MADE STATES
freed2003
Member
Member
Posts: 202
Joined: November 3rd, 2015, 3:00 pm
Division: C
State: CA
Has thanked: 9 times
Been thanked: 6 times

Re: Protein Modeling C

Post by freed2003 »

Does anyone know if for the competition they use the in-browser Jmol or the program?
BEARSO/MIT/High Desert/Regionals/State?
Cybersecurity 3/ /2/1
Codebusters 6/2/1/1
Circuit lab 77/20/3/1
Machines / /2/1
freed2003
Member
Member
Posts: 202
Joined: November 3rd, 2015, 3:00 pm
Division: C
State: CA
Has thanked: 9 times
Been thanked: 6 times

Re: Protein Modeling C

Post by freed2003 »

MacintoshJosh wrote:
meierfra wrote:
greenMountainCoffee wrote:
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.
Yes, this is something extremely confusing, but do not change the length from 168cm. The MSOE site states:
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. This section is 84 amino acids long and will require a toober that is 168cm long at the scale of 1 amino acid = 2cm.
It says that the section is 84 amino acids long, which is really confusing since 1-85 is 85 amino acids long, not 84. This means that either amino acid 1 or 85 would have to be omitted to fit the 84 amino acids. For invitationals we just snipped off the last amino acid and didn't get any points off. I'm not saying you should do that either, but you need to make sure you keep the length at 168cm. Sorry if this wasn't helpful but I'm hoping someone knows a complete explanation to this.
Don't quote me on this but I think the way it works is that the numbers represent the starting point of the residue and not the residue themselves(or something similar). For example note that on the 168cm model you make 85 marks if you count both ends but only 84 sections are created, each one representing a residue.

Or it could be like each mark represents a residue, in which case there are going to be 85 residues on your model and it's possible whoever was writing the MSOE website got lazy and say the 168 and 2 so they just divided them without thinking.
BEARSO/MIT/High Desert/Regionals/State?
Cybersecurity 3/ /2/1
Codebusters 6/2/1/1
Circuit lab 77/20/3/1
Machines / /2/1
User avatar
RRapples
Member
Member
Posts: 15
Joined: November 8th, 2016, 3:20 pm
Division: C
State: NJ
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by RRapples »

The Rules Manual states that "Each participant must bring a pencil or pen for the exam, a marker for marking the toobers, a metric ruler with cm marks, and one 8.5” x 11” sheet of paper ...". Does that mean each team member has to bring in these supplies? I don't recall teams in previous years bringing in multiple reference sheets.
JP Stevens 2020
Medals: 3 Regions, 2 Invitationals, 4 States
2016-17: Microbe
2017-18: Ecology, Herpetology, Microbe, Protein
2018-19: A&P, Designer Genes, Experimental Design, Herpetology, Protein, Science Quiz Bowl
2019-20: Designer Genes, Experimental Design, Ornithology, Protein
Anomaly
Exalted Member
Exalted Member
Posts: 642
Joined: February 17th, 2017, 10:46 am
Division: C
State: PA
Pronouns: She/Her/Hers
Has thanked: 4 times
Been thanked: 10 times

Re: Protein Modeling C

Post by Anomaly »

RRapples wrote:The Rules Manual states that "Each participant must bring a pencil or pen for the exam, a marker for marking the toobers, a metric ruler with cm marks, and one 8.5” x 11” sheet of paper ...". Does that mean each team member has to bring in these supplies? I don't recall teams in previous years bringing in multiple reference sheets.
I believe there was a clarification on soinc.org regarding this... and it says that if you have a team of 3, you are in fact allowed to bring three reference sheets. If you only have two people competing, then only 2 pieces of paper, and so on.
Orefield MS SO 2015-2018, Parkland HS SO 2019-2020
Medal/Ribbon Count
Invitational: 25
Regional: 16
State: 7
y o i n k s
Events: Anatomy and Physiology, Codebusters, Designer Genes, Protein Modeling
don't look at this its fake news now
User avatar
JoeyC
Member
Member
Posts: 307
Joined: November 7th, 2017, 1:43 pm
Division: Grad
State: TX
Has thanked: 503 times
Been thanked: 73 times

Re: Protein Modeling C

Post by JoeyC »

Anomaly
Exalted Member
Exalted Member
Posts: 642
Joined: February 17th, 2017, 10:46 am
Division: C
State: PA
Pronouns: She/Her/Hers
Has thanked: 4 times
Been thanked: 10 times

Re: Protein Modeling C

Post by Anomaly »

JoeyC wrote:That doesn't seem right https://www.soinc.org/events/rules-clarifications
Er, I meant an FAQ. sorry about that
Orefield MS SO 2015-2018, Parkland HS SO 2019-2020
Medal/Ribbon Count
Invitational: 25
Regional: 16
State: 7
y o i n k s
Events: Anatomy and Physiology, Codebusters, Designer Genes, Protein Modeling
don't look at this its fake news now
UTF-8 U+6211 U+662F
Exalted Member
Exalted Member
Posts: 1597
Joined: January 18th, 2015, 7:42 am
Division: C
State: PA
Has thanked: 6 times
Been thanked: 15 times

Re: Protein Modeling C

Post by UTF-8 U+6211 U+662F »

Anomaly wrote:
JoeyC wrote:That doesn't seem right https://www.soinc.org/events/rules-clarifications
Er, I meant an FAQ. sorry about that
That FAQ is for Forensics, but something similar probably applies.
Post Reply

Return to “2019 Lab Events”

Who is online

Users browsing this forum: No registered users and 1 guest