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Re: Protein Modeling C [NY Trial]

Posted: February 1st, 2010, 8:53 pm
by batmankiller
lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?

Re: Protein Modeling C [NY Trial]

Posted: February 3rd, 2010, 5:22 pm
by Phenylethylamine
lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?
For the on-site build at the competition, they will tell you which side chains to show, and give you little foam representations of those side chains to use. You will not have to decide what's important.

I found various information about important side chains simply by following the links listed in the event rules; the MSOE site mentioned there has several helpful links, including one that provided me with most of my information about side chains important to the protein's function. Alternately, you could try googling "structure of influenza hemagglutinin", since that is the protein we're working with.

Re: Protein Modeling C [NY Trial]

Posted: March 9th, 2010, 1:22 pm
by ahage16
lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?
For the on-site build at the competition, they will tell you which side chains to show, and give you little foam representations of those side chains to use. You will not have to decide what's important.

I found various information about important side chains simply by following the links listed in the event rules; the MSOE site mentioned there has several helpful links, including one that provided me with most of my information about side chains important to the protein's function. Alternately, you could try googling "structure of influenza hemagglutinin", since that is the protein we're working with.
What exact links on the MSOE site did you use to find the information about the important sidechains?

Re: Protein Modeling C [NY Trial]

Posted: March 9th, 2010, 3:28 pm
by Phenylethylamine
lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?
For the on-site build at the competition, they will tell you which side chains to show, and give you little foam representations of those side chains to use. You will not have to decide what's important.

I found various information about important side chains simply by following the links listed in the event rules; the MSOE site mentioned there has several helpful links, including one that provided me with most of my information about side chains important to the protein's function. Alternately, you could try googling "structure of influenza hemagglutinin", since that is the protein we're working with.
What exact links on the MSOE site did you use to find the information about the important sidechains?
It says, "View David Marcey's Molecular Museum page", and links to http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html. That's the most helpful one.

Re: Protein Modeling C [NY Trial]

Posted: March 10th, 2010, 5:51 pm
by Phenylethylamine
In Jmol, you can type "select sheets" and then color them to see the beta sheets, and "select helix" and then color to see the helices. The standard color for beta sheets is yellow, and for helices some type of red, but it's really irrelevant- as long as you choose a different color from the rest of your file, you'll be able to see exactly where they start and end.

The cross-linkers are for structural purposes only, so you can put them wherever you need them to stabilize your model.

To show important sidechains, you can use anything that will attach to the toober lol; it can represent the actual shape of the sidechain, but it doesn't have to. The shapes of the sidechains can be found at http://www.3dmoleculardesigns.com/AASK/ ... 20List.pdf, if you want your sidechains to actually represent the real shape. I've seen people use pushpins- just to show where the sidechains are, without the shape- model magic, pipe cleaners, ribbon (again, more for placement than shape), and tons of other things.

Yes, 1-160 refers to the amino acid numbers, and yes, blue goes at the starting point- the amino terminus- and red goes at the end point- the carboxy terminus.

When you put those sidechains on your computer model (for example, "select*b and his106 and sidechain", "wireframe 250"), you'll be able to see exactly where they are, and that the site (http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html) is accurate.
This is some advice I gave gsheni in answer to their questions, which I thought could be helpful to other people doing the event as well.

Re: Protein Modeling C [NY Trial]

Posted: March 16th, 2010, 1:13 pm
by sciolykid101
Did you guys use a 10 ft minitoober or some other structure to base your model on (for the pre-build portion)?

Re: Protein Modeling C [NY Trial]

Posted: March 16th, 2010, 5:38 pm
by Phenylethylamine
Did you guys use a 10 ft minitoober or some other structure to base your model on (for the pre-build portion)?
I was given a mini-toober of the exact right length (320 cm, somewhat more than ten feet) by my coach, who received it from MSOE (the organization sponsoring the event). I don't know what he had to do to get them to send it to him, but he didn't buy it- part of MSOE's sponsorship is that they spot everyone the mini-toobers.

Re: Protein Modeling C [NY Trial]

Posted: March 19th, 2010, 11:20 pm
by kwijiborjt
I ran this event at the RCS invitational... i think it's a great event! It's a huge, but i think it's very much in the creative spirit of science olympiad. How have your experiences been?

Re: Protein Modeling C [NY Trial]

Posted: March 20th, 2010, 12:56 pm
by johngrant
Is there a site showing how to use JMOL, for example, how to select and view a particular chain? This does not appear to work with the GUI within the JMOL tool.
A presenter showing the tool said "restrict" when she was keying in data on a scioly JMOL tutorial, but there wasn't any depth to this. Outlining the syntax and basic command structure would be helpful.An old manual guidance led me to believe Restrict[*b] would work but the JMOL app rejected this command.
Thanks!

Re: Protein Modeling C [NY Trial]

Posted: March 21st, 2010, 9:23 am
by Phenylethylamine
Is there a site showing how to use JMOL, for example, how to select and view a particular chain? This does not appear to work with the GUI within the JMOL tool.
A presenter showing the tool said "restrict" when she was keying in data on a scioly JMOL tutorial, but there wasn't any depth to this. Outlining the syntax and basic command structure would be helpful.An old manual guidance led me to believe Restrict[*b] would work but the JMOL app rejected this command.
Thanks!
If you go to http://cbm.msoe.edu/stupro/so/index.html and open the "2010 Pre-build Competition Environment" in the sidebar on the left, right above the screen showing the protein should be a link to a "Jmol Quick Reference Sheet", or something to that effect. It's a PDF that outlines the basic commands used in Jmol. That might be what you're looking for.

The "restrict" command is in fact what you want if you're trying to select and view only a particular subset of the protein, but the brackets are unnecessary. Just "restrict*b" or "restrict *b" (the space has no effect) will show only chain B.
The asterisk refers to a chain. To restrict your view even further, you would use, for example, "restrict*b and 1-160", where "1-160" refers to the range of numbers of amino acid residues within chain B you want to show.
If you wanted to show multiple chains or multiple ranges of residues, you would use "or", as in "restrict*b or *d".
If you're using an "and" and an "or" in the same command, you might need parentheses (not brackets) to specify which goes with what; e.g., "restrict(*b or *d) and 1-160" would show you residues 1-160 of chain B and residues 1-160 of chain D, while "restrict*b or (*d and 1-160)" would show you all of chain B and residues 1-160 of chain D.

Another tip: after restricting your view to any subset of the protein, I recommend using the "center" command to avoid wrestling with the small peripheral part of the PDB file you're viewing.
The default is for the center of rotation of the file to be the center of mass of the whole thing, but if you're only looking at a part of it on one edge, you don't really want it rotating around that point, because then in order to see the other side of your little part, you have to swing it all the way around that center. Some angles of viewing aren't even possible that way, because your part would be off-screen when you've got it sufficiently zoomed in to see the details.
Therefore, it can be very useful to add "center*b" if you're viewing chain B, or "center*b and 1-160" if you just restricted it to chain B and 1-160 (i.e., whatever you just put in the "restrict" command, use the same thing in the "center" command). This will save you a lot of annoyance.