Protein Modeling C

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CookiePie1
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Re: Protein Modeling C

Post by CookiePie1 » February 11th, 2020, 5:42 pm

unknownuser2 wrote:
February 11th, 2020, 5:26 pm
Hi all,

My regional doesn't run protein modeling, so I'm in the midst of getting ready for the state-level as my first go around this year. Last year in NYS, the ES's used Jsmol to do the onsite build, is it likely that the visualization part of the test will also be in Jsmol as well, or should I expect them to switch over to Jmol for this year.

Doubt anyone has explicit answers, however any thoughts would be greatly appreciated.
it depends on whether or not the ES decides to use the test provided by MSOE or to write their own test and jmol. If they write their own tests then it'll probably be in Jmol, but if they use the MSOE test it'll probably be in the online jsmol.
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Re: Protein Modeling C

Post by svph300 » February 11th, 2020, 5:44 pm

unknownuser2 wrote:
February 11th, 2020, 5:26 pm
Hi all,

My regional doesn't run protein modeling, so I'm in the midst of getting ready for the state-level as my first go around this year. Last year in NYS, the ES's used Jsmol to do the onsite build, is it likely that the visualization part of the test will also be in Jsmol as well, or should I expect them to switch over to Jmol for this year.

Doubt anyone has explicit answers, however any thoughts would be greatly appreciated.
Hi!

Since you're expected to know the commands for both Jmol and Jsmol, I recommend being familiar with both systems. I think that practicing with only one will ultimately put you at a disadvantage.
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Re: Protein Modeling C

Post by unknownuser2 » February 11th, 2020, 6:05 pm

Ok thanks to both of you!

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Re: Protein Modeling C

Post by eagerlearner102 » February 11th, 2020, 6:43 pm

They said that for the regional, only the alpha carbon backbone is judged. Does that mean it is not necessary to add decorations on the protein (side chains, DNA) or the decorations are needed at regional level? Also, is a flashcard needed for the regional?
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Re: Protein Modeling C

Post by sciencegirl03 » February 11th, 2020, 8:28 pm

unknownuser2 wrote:
February 11th, 2020, 5:26 pm
Hi all,

My regional doesn't run protein modeling, so I'm in the midst of getting ready for the state-level as my first go around this year. Last year in NYS, the ES's used Jsmol to do the onsite build, is it likely that the visualization part of the test will also be in Jsmol as well, or should I expect them to switch over to Jmol for this year.

Doubt anyone has explicit answers, however any thoughts would be greatly appreciated.
I'm also wondering the same. Both have largely the same functioning, but I still find Jmol easier to work with. The invitationals I have been to all used Jsmol except 1 that used Jmol, so I'm not sure what to expect either. I'm guessing Jsmol though, since states are probably regulated by the CBM and they prefer it.
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Re: Protein Modeling C

Post by MacintoshJosh » February 12th, 2020, 6:24 pm

eagerlearner102 wrote:
February 11th, 2020, 6:43 pm
They said that for the regional, only the alpha carbon backbone is judged. Does that mean it is not necessary to add decorations on the protein (side chains, DNA) or the decorations are needed at regional level? Also, is a flashcard needed for the regional?
[4.b.iii.(2)] For Regional competitions, scoring will be based primarily on the accuracy of the 3D folded structure of the alpha-carbon backbone of the protein (secondary and tertiary structures).
I think it's important to note that the rules uses the word "primarily", implying that the backbone doesn't account for the entire score of the pre-build, just a large portion. If you're in a pinch and don't have time to add the decorations, I think you should be fine, only losing minimal points. However, if you want to max out your points I would definitely add the extra decorations and write a notecard as well. At my regional competition they asked for the notecard and I'm pretty sure it was graded - it was also CBM regulated.
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Re: Protein Modeling C

Post by eagerlearner102 » February 13th, 2020, 5:16 pm

For Jmol, I am kind of confused between the cpk and spacefill command for atom display. I notice that cpk is used for alpha helix. can someone explain the difference and the advantages?
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Re: Protein Modeling C

Post by CookiePie1 » February 13th, 2020, 5:48 pm

eagerlearner102 wrote:
February 13th, 2020, 5:16 pm
For Jmol, I am kind of confused between the cpk and spacefill command for atom display. I notice that cpk is used for alpha helix. can someone explain the difference and the advantages?
well, spacefill is a display format. it controls the shape of the molecules in question and will display each selected atom as a sphere of whatever size you want (usually dispayed at 1.25).

cpk is a color scheme. When you use the "color cpk" command then it colors the selected atoms according to their element - Carbon=grey, Nitrogen=blue, oxygen=red, sulfur=yellow, phosphorous=orange, etc. idk what you mean by cpk being used for an alpha helix. If i wanted to seperate the structures by color i would use "color structure".
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Re: Protein Modeling C

Post by unknownuser2 » February 14th, 2020, 9:17 pm

Hi all,

Just as a general guideline, about how long do people usually spend folding their protein backbones (aka how long do you spend on the pre-build-not counting the functional features)? I started working on mine recently and in the year since I last touched a mini-toober, I forgot how bad I am at folding, and am just trying to gauge wether I’m spending about the average on the build, or way too long.

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Re: Protein Modeling C

Post by Chameleon02 » February 15th, 2020, 12:43 am

Hey guys. How do I find out how many chains are in a structure?
How do I find the widest width of a protein?
How do I find how many polymers a structure contains?
Thanks!
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