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Protein Modeling C

Posted: July 2nd, 2011, 7:49 pm
by Jim_R

Re: Protein Modeling C

Posted: August 29th, 2011, 1:27 pm
by Phenylethylamine
Based on the way the CBM site was set up, I was under the impression that XIAP was going to be the prebuild, but apparently it's actually caspase-3.

Also, despite the fact that the Science Olympiad link in the header on the 3D Molecular Designs website still says 2010-2011, the page has already been updated for 2012. Prebuild kits will be available for order starting September 1st.

Re: Protein Modeling C

Posted: August 30th, 2011, 6:33 am
by Starapollo1
So basically, we are constructing two distinct polypeptides that make up the protein as a whole?? Ionly ask cause the jmol has two seperate mini toobers... if i'm off base please help me out!

Re: Protein Modeling C

Posted: August 30th, 2011, 12:22 pm
by EastStroudsburg13
What might end up happening is that we just model one of the two. I haven't looked at the jmol yet, but depending on how long each individual polypeptide is, they might just have us model one or a section of one, which is what happened last year.

Re: Protein Modeling C

Posted: August 30th, 2011, 4:13 pm
by butter side up
It appears that the entire protein is composed of 6 polypeptide chains, and we are building two of them. From what the website said, these are found by selecting a and selecting b.
On a related note, does anyone know how to select and isolate two separate chains at once? I can get it to show only a, and only b, but not both at once without all the other chains.

Re: Protein Modeling C

Posted: August 30th, 2011, 4:27 pm
by TheGenius
Try "restrict *A or *B". That should work, but I'm not able to test it currently.

Re: Protein Modeling C

Posted: August 30th, 2011, 4:48 pm
by butter side up
Try "restrict *A or *B". That should work, but I'm not able to test it currently.
Thanks! That does the job very well... it should come in handy.
So I am thinking that the best way to work with the two proteins will be to suspend them both from a framework with fishing line or something, rather than propping it up with skewers in it, as we did with klf4. How do you guys support your proteins? Because the suspension looks like our best plan for now, but we are worried about transport and whatnot.

Re: Protein Modeling C

Posted: September 1st, 2011, 10:32 am
by Starapollo1
Try "restrict *A or *B". That should work, but I'm not able to test it currently.
Thanks! That does the job very well... it should come in handy.
So I am thinking that the best way to work with the two proteins will be to suspend them both from a framework with fishing line or something, rather than propping it up with skewers in it, as we did with klf4. How do you guys support your proteins? Because the suspension looks like our best plan for now, but we are worried about transport and whatnot.
We supsended ours last year with fishing line. Be forwarned, suspendeding can be quite frustrating lol there will be some trial and error to get it to suspend right and make sure you bring extra fish line with you to the competitions so that you can patch it up before you impound it! lol

Re: Protein Modeling C

Posted: September 1st, 2011, 6:00 pm
by Phenylethylamine
Try "restrict *A or *B". That should work, but I'm not able to test it currently.
Thanks! That does the job very well... it should come in handy.
So I am thinking that the best way to work with the two proteins will be to suspend them both from a framework with fishing line or something, rather than propping it up with skewers in it, as we did with klf4. How do you guys support your proteins? Because the suspension looks like our best plan for now, but we are worried about transport and whatnot.
I use 22-gauge jewelry wire for everything- the advantage is that it's strong enough to prop the protein up from underneath (at least, if you twist a couple strands together), but also unobtrusive enough that it doesn't obscure the protein if you use it to suspend your model. It's also a lot more durable and solid than fishing line, so you're less likely to have problems with it breaking or tangling.

Re: Protein Modeling C

Posted: September 1st, 2011, 7:26 pm
by starpug
Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?