Protein Modeling C

[Phenylethylamine]

I'm having incredible difficulties isolating the two polypeptides we are supposed to model... Upon going to the the prebuild page: [urlhttp://cbm.msoe.edu/includes/jmol/SOJmols/2012PreBuild.html[/url], I tried "restrict chain A" and "restrict chain B" along with multiple variations of the command... and I can't seem to get it to work... the answer is probably really simple but I just can't seem to figure it out.

First, the command to restrict to just chain A would be "restrict *a"; Jmol doesn't know the word "chain".

Second, "restrict" gets rid of everything that isn't included in your argument: if you restrict to chain A and then restrict to chain B, there won't be anything left – you got rid of everything that wasn't chain A, then everything that wasn't chain B, so you'll end up with just an empty screen. If you want chain A and chain B onscreen at the same time, you'll need "restrict *a or *b".

[ironchef48]

Where do you find information about the "protein Story" we are supposed to illustrate? I've read the article about Caspases and found a few unique structures by laying around with jmol, but i feel like I'm missing something because I can't correlate these structures to anything.
(For instance, the molecule pictured alongside the protein in the Caspase-3 graphic on the PDB page)

[Starapollo1]

I'm having incredible difficulties isolating the two polypeptides we are supposed to model... Upon going to the the prebuild page: [urlhttp://cbm.msoe.edu/includes/jmol/SOJmols/2012PreBuild.html[/url], I tried "restrict chain A" and "restrict chain B" along with multiple variations of the command... and I can't seem to get it to work... the answer is probably really simple but I just can't seem to figure it out.

First, the command to restrict to just chain A would be "restrict *a"; Jmol doesn't know the word "chain".

Second, "restrict" gets rid of everything that isn't included in your argument: if you restrict to chain A and then restrict to chain B, there won't be anything left – you got rid of everything that wasn't chain A, then everything that wasn't chain B, so you'll end up with just an empty screen. If you want chain A and chain B onscreen at the same time, you'll need "restrict *a or *b".

Thanks!! Much appreciated

[butter side up]

Where do you find information about the "protein Story" we are supposed to illustrate? I've read the article about Caspases and found a few unique structures by laying around with jmol, but i feel like I'm missing something because I can't correlate these structures to anything.
(For instance, the molecule pictured alongside the protein in the Caspase-3 graphic on the PDB page)

The molecular story aspect of it is mainly centered on the function of the protein and the other proteins or molecules it interacted with. Last year, this meant that the protien interacted with zinc ions and DNA, both of which we included in our model. In addition, it is important to explain them on your notecard. We generally gave samples of all our additions and whatnot taped to the front with labels [ie. a small piece of the n- and c-termini, a H-bond, the ribbon we used to mark alpha helices, etc...] and devoted the back to an explanation of our marked structures and their importance, as well as an explanation of the overall function of the protein. If you mentioned something about Nic, the boy that we have so much stuff on, that would probably be a good part, as well as the function of the proteins and the molecules it interacts with.

[akatsuki9]

I had a question on the invite that had to do with Nicholas Volker 2009...

[Phenylethylamine]

I had a question on the invite that had to do with Nicholas Volker 2009...

That's hardly surprising, given that his story was the first thing posted on the CBM site.

[EastStroudsburg13]

I have a question regarding Chain A. In the vizualization, residues 207-225 are selected as part of an alpha helix. However, in the image for the sequence, there is a gap at residue 221, and a second helix that enxtends to 226.

Also, in the vizualization, the area in question doesn't really look like a helix: it just happens to be colored that way when i do "select helix... color red". I'm color-coding my Toober for the secondary structures, so my question is, do I go with the jmol or the PDB sequence? I'm thinking the jmol personally, since that's officially in the rules, but I wanted to see what other people think and if anyone else has seen this.

[Starapollo1]

I have a question regarding Chain A. In the vizualization, residues 207-225 are selected as part of an alpha helix. However, in the image for the sequence, there is a gap at residue 221, and a second helix that enxtends to 226.

Also, in the vizualization, the area in question doesn't really look like a helix: it just happens to be colored that way when i do "select helix... color red". I'm color-coding my Toober for the secondary structures, so my question is, do I go with the jmol or the PDB sequence? I'm thinking the jmol personally, since that's officially in the rules, but I wanted to see what other people think and if anyone else has seen this.

I don't know about invitationals, but the national event supervisor simply goes to jmol and then prints it off with her 3D printer. That being the case, I would build my model as close to the jmol as possible.

[EastStroudsburg13]

I have submitted an FAQ to soinc.org and am currently anticipating a response. However, I'm leaning toward coloring the helix based on jmol, and folding the part that's not really a helix the way it is on the visualization.

On a side note, I folded chain B this weekend. I felt accomplished.

[akatsuki9]

Chain B is actually the easier chain to fold.