Page 11 of 28

Re: Protein Modeling C

Posted: December 6th, 2018, 9:18 am
by tm-scioli
OK thank you!
But what other add ons would you use beyond that?

Re: Protein Modeling C

Posted: December 13th, 2018, 1:42 pm
by DaedalusMinor
Do you guys think that putting chunks of CRISPR Cas9 sequences on the model would be a good idea? Like attaching small lengths of toobers to anti-Crispr, wherever it is bonded to Cas9.

Much love from,
Michael Cera and Baljeet Tjinder <3 <3 <3 <3

Re: Protein Modeling C

Posted: December 13th, 2018, 2:36 pm
by luanne
Guys: is your prebuild toober that you ordered correct? ours is 164 cm.
Also: how do you identify at which residue the helix/sheet starts/ends?

Re: Protein Modeling C

Posted: December 13th, 2018, 3:45 pm
by platypusomelette
Anyone have any ideas for how to display the cas9? Should I just take a knife to a chunk of styrofoam or something lol

Re: Protein Modeling C

Posted: December 13th, 2018, 4:25 pm
by CookiePie1
Do you guys think that putting chunks of CRISPR Cas9 sequences on the model would be a good idea? Like attaching small lengths of toobers to anti-Crispr, wherever it is bonded to Cas9.

Much love from,
Michael Cera and Baljeet Tjinder <3 <3 <3 <3
You should only do so if those parts are important to how the Anti-CRISPR protein disables the function of the Cas9 protein.
Guys: is your prebuild toober that you ordered correct? ours is 164 cm.
Also: how do you identify at which residue the helix/sheet starts/ends?
If you ordered your kit from 3D Molecular Designs, it should be correct. In the Online Prebuild Environment, Once you have narrowed it down to the part you'd like to model, if you wave your mouse over the structure, it'll tell you which residue you are waving over.
Anyone have any ideas for how to display the cas9? Should I just take a knife to a chunk of styrofoam or something lol
You aren't required to display the Cas9 protein itself, but you can if you want. Since it's a creative addition, you are at liberty to display it in any form you would like. If you think sticking a knife in some styrofoam is a good way to do it, then go ahead.

Re: Protein Modeling C

Posted: December 14th, 2018, 9:13 am
by meierfra
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

Re: Protein Modeling C

Posted: December 24th, 2018, 5:55 am
by MacintoshJosh

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.

Re: Protein Modeling C

Posted: December 27th, 2018, 6:59 pm
by platypusomelette
Anyone know a good convenient place to learn about the amino acids in detail?

Re: Protein Modeling C

Posted: December 30th, 2018, 8:21 pm
by freed2003
Does anyone know if for the competition they use the in-browser Jmol or the program?

Re: Protein Modeling C

Posted: December 30th, 2018, 8:23 pm
by freed2003

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.