Protein Modeling C

Gearbox
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Re: Protein Modeling C

Postby Gearbox » October 17th, 2014, 1:22 pm

I don't seem to have that problem. I've attached a screenshot so you can see if we are doing the same thing.
That's the dimer, you only want to model biomolecule a
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alwaysmatts
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Re: Protein Modeling C

Postby alwaysmatts » October 17th, 2014, 2:27 pm

Hey I'm totally new to this event. So will we know exactly which protein will be build on site or nah
Last edited by alwaysmatts on October 18th, 2014, 6:53 pm, edited 1 time in total.
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Re: Protein Modeling C

Postby Tony116 » October 17th, 2014, 2:37 pm

Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.
Ok so I've marked all my 2cm markings on my protein, and I'm wondering how would you label each end cap? Since we're starting with 421, would the c terminus be 421 and then the end cap would be 560 plus the amino acid next to it? I'm still a little confused by that.

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Re: Protein Modeling C

Postby emmadej » October 20th, 2014, 6:52 pm

I don't seem to have that problem. I've attached a screenshot so you can see if we are doing the same thing.
Yeah, I have typed in exactly that in addition to restrict *A and nothing happened. Someone suggested elsewhere I might be using a 'training model', but the JMOL I downloaded was off the website given to us by the SciOly page...

If there are indeed 2 versions of JMOL, could someone send me the real one? The one I have seems to do all commands like "cartoon on, wireframe off, select helix, color red," etc.

:C

Whenever I type in "restrict (blah blah atom numbers i need)" it says 0 atoms selected and poof no more protein :C


Also, is there a way to get cheaper materials for the pre-build model than the 24$ one on the website?
I'd like to keep that snazzy tuber thing. c:

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Re: Protein Modeling C

Postby EastStroudsburg13 » October 20th, 2014, 10:28 pm

Just to make sure, are you using this link for the pre-build? I ask because someone else on chat had a very similar problem.
Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.
Ok so I've marked all my 2cm markings on my protein, and I'm wondering how would you label each end cap? Since we're starting with 421, would the c terminus be 421 and then the end cap would be 560 plus the amino acid next to it? I'm still a little confused by that.
What exactly do you mean by label? What I remember doing is marking everything and then putting the caps on, and then each cap ended up representing their respective termini. You might be doing a more involved labeling method, which is fine as long as you don't get carried away, but if the measurements work the same as they used to then each cap will count as one amino acid (i.e. 421 at beginning, 560 at end, you should not need 561)
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Re: Protein Modeling C

Postby JonB » October 21st, 2014, 4:40 am


Also, is there a way to get cheaper materials for the pre-build model than the 24$ one on the website?
I'd like to keep that snazzy tuber thing. c:
Here is an interesting material that we REALLY like to use for this event. It is sturdy, and fairly easy to work with:

http://www.niteize.com/product/Gear-Tie-64.asp

You will have to figure out how to connect several of them together to be long enough- but we really like them. They have them at Home Depot if you want to take a look at them. Is it collectively going to be cheaper than the Tubers? Well, the shipping from 3D molecular designs is really pricey, so if you purchase at Home Depot it might save some bucks.

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Re: Protein Modeling C

Postby fantasyfan » October 21st, 2014, 4:22 pm

Yeah, I have typed in exactly that in addition to restrict *A and nothing happened. Someone suggested elsewhere I might be using a 'training model', but the JMOL I downloaded was off the website given to us by the SciOly page...

If there are indeed 2 versions of JMOL, could someone send me the real one? The one I have seems to do all commands like "cartoon on, wireframe off, select helix, color red," etc.

:C

Whenever I type in "restrict (blah blah atom numbers i need)" it says 0 atoms selected and poof no more protein :C
The site where I downloaded my version of JMOL is [http://cbm.msoe.edu/includes/modules/jm ... arted.html]. The site EastStroudsburg mentioned, [http://cbm.msoe.edu/scienceOlympiad/des ... build.html], follows the same commands as the earlier link I gave.
I had the same issue that you had, but my problem was fixed when I realized that A needed to be capitalized.
Try copying "restrict *A and 421-560" into your command console, and see if that works.
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

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Re: Protein Modeling C

Postby Gemma W » October 23rd, 2014, 8:39 am

Hey I'm totally new to this event. So will we know exactly which protein will be build on site or nah
All proteins for on-site and pre-build can be found on the CBM website, and are posted on the protein wiki under year-specific information.
Last edited by Gemma W on October 23rd, 2014, 9:29 am, edited 1 time in total.
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Re: Protein Modeling C

Postby colorado mtn science » October 23rd, 2014, 9:02 am

When the fokI endonuclease protein is loaded on jmol, first we use the console to eliminate all amino acids besides 421-560. Then, we are left with two biomolecules. At first they appeared to be the same, however, when selecting one of them to view, jmol displays biomolecule 2 as have 53 more atoms than biomolecule 1. Does anyone know which biomolecule we are supposed to be modeling our protein after? Thank you!
You need to specify that you want chain A,
Restrict *A
Don't forget to capitalize the "A"
It always works for me if I don't capitalize the a

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Re: Protein Modeling C

Postby colorado mtn science » October 23rd, 2014, 9:14 am

Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.
Ok so I've marked all my 2cm markings on my protein, and I'm wondering how would you label each end cap? Since we're starting with 421, would the c terminus be 421 and then the end cap would be 560 plus the amino acid next to it? I'm still a little confused by that.
realize that the primary structure of proteins is listed from n terminus to c terminus so the lowest number (in this case 421) should be the n terminus, not the c terminus.


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