Protein Modeling C

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JoeyC
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Re: Protein Modeling C

Postby JoeyC » October 21st, 2018, 1:29 pm

Should I just be getting one protein chain (yes this was mentioned earlier, but that was about the CRISPR, not Anti-CRISPER protein)?
And of the chain, which part contains the nuclease?
And should I build the Viral RNA, Tracer and CRISPR RNA as side chains?
Thanks!
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Re: Protein Modeling C

Postby platypusomelette » October 23rd, 2018, 4:28 am

JoeyC wrote:Should I just be getting one protein chain (yes this was mentioned earlier, but that was about the CRISPR, not Anti-CRISPER protein)?
And of the chain, which part contains the nuclease?
And should I build the Viral RNA, Tracer and CRISPR RNA as side chains?
Thanks!

FYI "side chain" usually refers to the additions on amino acids, not pieces of protein, those would be something like "subunits" or "domains". I think it would be a good idea to build those additional parts as well
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Re: Protein Modeling C

Postby platypusomelette » October 27th, 2018, 10:29 am

http://cbm.msoe.edu/modGallery/ScienceO ... ges/33.jpg

Anyone know if this is how they grade? What's that model he's holding, and where does that model come from? Also do any event supervisors here know exactly what the process of scoring is like?
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Re: Protein Modeling C

Postby JoeyC » November 1st, 2018, 6:01 am

So do I build the Anti Crispr and Crispr or just the anti Crispr? :lol:
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Re: Protein Modeling C

Postby CookiePie1 » November 1st, 2018, 2:47 pm

JoeyC wrote:So do I build the Anti Crispr and Crispr or just the anti Crispr? :lol:


I believe it is just the Anti-CRISPR for the prebuild.
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Re: Protein Modeling C

Postby MacintoshJosh » November 8th, 2018, 1:02 pm

Why does typing "select hydrogen" show 0? Shouldn't there be hydrogen atoms in every amino acid?

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Re: Protein Modeling C

Postby meierfra » November 10th, 2018, 1:13 pm

Looking at the CRISPR page of the Wiki https://scioly.org/wiki/index.php/Protein_Modeling/CRISPR, it says the Anti-CRISPR pre-build is pdb ID 5xn4. The rules clarification says it's 5vw1. The Wiki page is wrong? Are those other CRISPR IDs correct?

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Re: Protein Modeling C

Postby Unome » November 10th, 2018, 2:41 pm

meierfra wrote:Looking at the CRISPR page of the Wiki https://scioly.org/wiki/index.php/Protein_Modeling/CRISPR, it says the Anti-CRISPR pre-build is pdb ID 5xn4. The rules clarification says it's 5vw1. The Wiki page is wrong? Are those other CRISPR IDs correct?

I don't know the details, but I would assume the rules clarification is accurate.
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Jmol/Smol program

Postby LowBlue1 » November 15th, 2018, 2:51 pm

Do we need to have this software downloaded on our computers?

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Re: Protein Modeling

Postby Unome » November 15th, 2018, 5:13 pm

LowBlue1 wrote:Do we need to have this software downloaded on our computers?

Jmol/Smol is useful to have downloaded to help you understand it. It's not technically required, but I can't see a team doing very well without having it. Although, I think it's browser-based as well.
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Re: Protein Modeling C

Postby rhkoulen » November 16th, 2018, 9:52 pm

I just picked up Jmol and I have 0 grasp on biology much less protein modeling, but it's really fun so far.


I really could use some help with Jmol. Is there a PDB reference code I can use to get CRISPR Cas9? I've searched around, but I can only find Cas9 attached to viral DNA strands.

hepl

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Re: Protein Modeling C

Postby rhkoulen » November 16th, 2018, 9:56 pm

rhkoulen wrote:I just picked up Jmol and I have 0 grasp on biology much less protein modeling, but it's really fun so far.


I really could use some help with Jmol. Is there a PDB reference code I can use to get CRISPR Cas9? I've searched around, but I can only find Cas9 attached to viral DNA strands.

hepl



hol up I'm dummm 4un3.pdb

ooooof

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Re: Protein Modeling C

Postby rhkoulen » November 16th, 2018, 10:08 pm

How can you convert the mess of 4un3 to something that doesn't give me a stroke when you look at it?

Any links to tutorials would be nice too thanks.

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Re: Protein Modeling C

Postby Limke » November 17th, 2018, 7:12 am

rhkoulen wrote:How can you convert the mess of 4un3 to something that doesn't give me a stroke when you look at it?

Any links to tutorials would be nice too thanks.


The MSOE website has a bunch of tutorials on how to use Jmol and restrict domains (removing all the residues you don't need, showing certain sidechains, restricting to just the backbone (2ndary structure)

http://cbm.msoe.edu/scienceOlympiad/participant3.php

Scroll down on that page and they should have links under their Advanced Jmol training guide, which I found particularly helpful!
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Re: Protein Modeling C

Postby rhkoulen » November 18th, 2018, 6:47 am

Limke wrote:
rhkoulen wrote:How can you convert the mess of 4un3 to something that doesn't give me a stroke when you look at it?

Any links to tutorials would be nice too thanks.


The MSOE website has a bunch of tutorials on how to use Jmol and restrict domains (removing all the residues you don't need, showing certain sidechains, restricting to just the backbone (2ndary structure)

http://cbm.msoe.edu/scienceOlympiad/participant3.php

Scroll down on that page and they should have links under their Advanced Jmol training guide, which I found particularly helpful!


Thank you so much!


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