It doesn't need to be installed, though. The file will run on any computer with Java installed, like the web version, even on differing operating systems.chalker wrote:TheGenius wrote:I am curious: Why do they make us use the applet version of Jmol instead of regular Jmol? Standalone Jmol is much better and more tolerable than the web version.
Probably because in many school computer labs it's hard to get administrator access in order to install new software. With the web version you can run it from virtually anywhere.
Protein Modeling C
- TheGenius
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Re: Protein Modeling C
Any opinions expressed by TheGenius are those of individual brain cells and not necessarily those of the brain as a whole. Use information provided at your own risk.
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- FullMetalMaple
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Re: Protein Modeling C
Slightly different from what you're asking, but I'm also curious - what did you think of how Jmol was set up at state? I found it surprisingly difficult to work with and wondered if anyone else had the same problem. I couldn't get different views without a weird zoom effect, which I've never experienced before. It might have been better with the regular version.TheGenius wrote:I am curious: Why do they make us use the applet version of Jmol instead of regular Jmol? Standalone Jmol is much better and more tolerable than the web version.
- Dragonshark
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Re: Protein Modeling C
The jmol at States was difficult to work with at times. I couldn't seem to center the display, unlike the jmol version I normally use, when I could click and hold to shift the display around without rotating it. Despite this being the same jmol version, this didn't seem to be a problem at Regionals.FullMetalMaple wrote:Slightly different from what you're asking, but I'm also curious - what did you think of how Jmol was set up at state? I found it surprisingly difficult to work with and wondered if anyone else had the same problem. I couldn't get different views without a weird zoom effect, which I've never experienced before. It might have been better with the regular version.TheGenius wrote:I am curious: Why do they make us use the applet version of Jmol instead of regular Jmol? Standalone Jmol is much better and more tolerable than the web version.
Also, a piece of advice for the onsite in general: Do a 'practice fold' of the onsite before competition, and include some reference photos of the practice model in your notes. This allows you to familiarize yourself with the general structure of the protein and will allow you to fold it much quicker and more accurately. Also, including the photos will give you another thing to reference during the competition, especially if you find the onsite jmol version clumsy to work with (like it did at States).
Nathan Hale HS SciO
2011 - Regionals/States: Anat/Phys [1/1!!!], Chem Lab [1/2]
2012 - Regionals/States: Chem Lab [1/6 >_< ], Forensics [2/1!!!], Protein [1/2], Team [9]
2013 - A/P, Chem Lab, 4N6, TPS, C/A (trial)
2011 - Regionals/States: Anat/Phys [1/1!!!], Chem Lab [1/2]
2012 - Regionals/States: Chem Lab [1/6 >_< ], Forensics [2/1!!!], Protein [1/2], Team [9]
2013 - A/P, Chem Lab, 4N6, TPS, C/A (trial)
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Re: Protein Modeling C
Hey, I'm just studying PARP-1 based off of 3OD8 and I see that they're a few ligands/amino acids (not sure what they are), but on proteopedia it calls them MSE can someone explain to me what exactly it is and if it has anything to do with the function of PARP...Thanks
2012 State:
1st Robot Arm
2nd Protein Modeling
3rd Microbe Mission
1st Robot Arm
2nd Protein Modeling
3rd Microbe Mission
- Rackis
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Re: Protein Modeling C
What's the difference between the beta-buldge and the standard beta strand and how would one show this on a model? Thanks.
2012 events[invitational, regional, state]: Gravity Vehicle[6th, 5th, X], Microbe Mission[4th, 3rd, 1st], Protein Modeling[6th, 5th, 1st], Water Quality[3rd, 5th, 1st]
2013 events[invitational, regional, state]: Gravity Vehicle[8th, ?, ?], A&P[7th, ?, ?], Water Quality[2nd, ?, ?]
2013 events[invitational, regional, state]: Gravity Vehicle[8th, ?, ?], A&P[7th, ?, ?], Water Quality[2nd, ?, ?]
- Phenylethylamine
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Re: Protein Modeling C
It doesn't matter exactly where in the amino acid you kink the Toober, but you should be consistent: adjacent kinks should be at the same point in the amino acids, so they fall 2cm apart.flyingwatermelon wrote:1) For the beta sheet are the "kinks" in the model that we place them exactly on the amino acid lines? |amino acid| 2cm
Most "correctly", the kink should occur at the point where the sidechain extends outward (which could be good to know if they give you a sidechain to show that falls somewhere in a beta strand), but I do not believe that this is part of the grading criteria. Could be good to keep in mind anyway, though.
You should try to follow what you see in Jmol as closely as possible. I recommend watching the video about folding 3D structure on the CBM site for more detail.flyingwatermelon wrote:2) For the rest of the structure that isn't beta sheets/pi helices/alpha helices, do we attempt to model them in the way Jmol has it arranged in backbone format? Or is it up to our discretion...
Note that the applet has improved considerably from last year: it used to be necessary to click "Execute" and then manually empty the field after each command.TheGenius wrote:I am curious: Why do they make us use the applet version of Jmol instead of regular Jmol? Standalone Jmol is much better and more tolerable than the web version.
Some school computer labs make it very hard even to save files locally (e.g., they require all users to save everything to flash drives), or do not allow files that could potentially contain applications to be saved.TheGenius wrote:It doesn't need to be installed, though. The file will run on any computer with Java installed, like the web version, even on differing operating systems.chalker wrote: Probably because in many school computer labs it's hard to get administrator access in order to install new software. With the web version you can run it from virtually anywhere.
Probably more importantly, though, standalone Jmol is not totally straightforward to download, and many event supervisors may not be inclined to go to the (relatively small, I admit) extra effort to put it on twenty or thirty computers when they're being provided with a webpage that they just have to open. Some may not even be aware that standalone Jmol is a thing that exists (which sounds scary, but it was actually primarily developed to be used as a web applet, so you could be completely aware of how it works and still not fully cognizant of the fact that there's a standalone version).
At NY States, they gave us the choice of using standalone or the webapp, which was a pleasant surprise. I used standalone, but it was nice to have both options, because when something weird and anomalous showed up in the structure (no spoilers), I could check that it was, in fact, part of the structure and not some artifact of the platform.
Excellent advice. If you don't have another Toober, you can do a "mental" practice fold: 'Here's a helix, and then there's a beta strand that comes around next to this other beta strand over here, and then they're parallel to the helix, and then this other helix is over here at this angle, about this far away...' Do that a few times, and the onsite will go much more quickly in competition (although this year's States onsite is tiny and pretty easy; it took me literally fifteen minutes to fold, although I then took another five or so to check my work really carefully. I assume this is why the NY State Protein supervisor limited it to two people at States this year).Dragonshark wrote:Also, a piece of advice for the onsite in general: Do a 'practice fold' of the onsite before competition, and include some reference photos of the practice model in your notes. This allows you to familiarize yourself with the general structure of the protein and will allow you to fold it much quicker and more accurately. Also, including the photos will give you another thing to reference during the competition, especially if you find the onsite jmol version clumsy to work with (like it did at States).
They are modified amino acids called selenomethionine (MSE being the three-letter code they use for this particular modified residue). This means that the sulfur normally in the methionine residue has been replaced with a selenium atom.GCXC wrote:Hey, I'm just studying PARP-1 based off of 3OD8 and I see that they're a few ligands/amino acids (not sure what they are), but on proteopedia it calls them MSE can someone explain to me what exactly it is and if it has anything to do with the function of PARP...Thanks
They are not normally present in PARP; this is a modification that the crystallographers made so they could do some kind of imaging based on the position of the selenium atoms (I'm not sure why selenium, but this was in the original citation for 3OD8, albeit somewhat buried in the Materials and Methods section). So sadly, no, they are not relevant to the function of PARP; it's another one of those changes (like taking out some of the cysteines in caspase-3 in 1I3O) that the researchers made to make it easier to get the correct structure.
As far as this event is concerned, beta bulges don't exist. A beta bulge is just a localized disruption of "normal" backbone structure that has hydrogen bonding roughly similar to what you find in a beta strand, but it really doesn't look that different from the rest of the backbone, and it doesn't appear in Jmol. They're interesting – you can read the Wikipedia article, which is pretty concise – but not relevant to the event.Rackis wrote:What's the difference between the beta-buldge and the standard beta strand and how would one show this on a model? Thanks.
In short, fold your beta strands as usual; don't worry about beta bulges at all.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
- Rackis
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Re: Protein Modeling C
Thanks Phenyl, but my state was today lol. Got first place anyhow though!Phenylethylamine wrote:As far as this event is concerned, beta bulges don't exist. A beta bulge is just a localized disruption of "normal" backbone structure that has hydrogen bonding roughly similar to what you find in a beta strand, but it really doesn't look that different from the rest of the backbone, and it doesn't appear in Jmol. They're interesting – you can read the Wikipedia article, which is pretty concise – but not relevant to the event.Rackis wrote:What's the difference between the beta-buldge and the standard beta strand and how would one show this on a model? Thanks.
In short, fold your beta strands as usual; don't worry about beta bulges at all.
2012 events[invitational, regional, state]: Gravity Vehicle[6th, 5th, X], Microbe Mission[4th, 3rd, 1st], Protein Modeling[6th, 5th, 1st], Water Quality[3rd, 5th, 1st]
2013 events[invitational, regional, state]: Gravity Vehicle[8th, ?, ?], A&P[7th, ?, ?], Water Quality[2nd, ?, ?]
2013 events[invitational, regional, state]: Gravity Vehicle[8th, ?, ?], A&P[7th, ?, ?], Water Quality[2nd, ?, ?]
- Infinity Flat
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Re: Protein Modeling C
I would assume that they are using selenium simply because it is directly below sulfur on the periodic table, and so is chemically very similar. There may be a little more subtlety to it, but that's the main gist of it.Phenylethylamine wrote:They are modified amino acids called selenomethionine (MSE being the three-letter code they use for this particular modified residue). This means that the sulfur normally in the methionine residue has been replaced with a selenium atom.GCXC wrote:Hey, I'm just studying PARP-1 based off of 3OD8 and I see that they're a few ligands/amino acids (not sure what they are), but on proteopedia it calls them MSE can someone explain to me what exactly it is and if it has anything to do with the function of PARP...Thanks
They are not normally present in PARP; this is a modification that the crystallographers made so they could do some kind of imaging based on the position of the selenium atoms (I'm not sure why selenium, but this was in the original citation for 3OD8, albeit somewhat buried in the Materials and Methods section). So sadly, no, they are not relevant to the function of PARP; it's another one of those changes (like taking out some of the cysteines in caspase-3 in 1I3O) that the researchers made to make it easier to get the correct structure.
(State, Nationals)
2013: Astro (2, 6) / Chem (2, 5) / Circuits (8, 36) / Diseases (1,1) / Fermi (N/A, 24) / Materials (1, N/A)
2012 : Astro (1, 11) / Chem (N/A, 13) / Diseases (3, 1) / Optics (2, 3) / Sounds (2, 1)
2011: Astro(2,11) / Diseases (1,27) / Optics (1,13) / Proteins (2,15)
2013: Astro (2, 6) / Chem (2, 5) / Circuits (8, 36) / Diseases (1,1) / Fermi (N/A, 24) / Materials (1, N/A)
2012 : Astro (1, 11) / Chem (N/A, 13) / Diseases (3, 1) / Optics (2, 3) / Sounds (2, 1)
2011: Astro(2,11) / Diseases (1,27) / Optics (1,13) / Proteins (2,15)
- Phenylethylamine
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Re: Protein Modeling C
Sorry, I understand why it's feasible to replace the sulfur with selenium; the part I'm not sure about is how they detect the position of the selenium atoms in particular. There's some structure determination method that uses the position of the selenium atoms – which apparently they can somehow determine more easily – to align the overall protein structure. I understand how they do the alignment once they have the positions of the selenium atoms, but I don't know what method they use to find those positions.Infinity Flat wrote:I would assume that they are using selenium simply because it is directly below sulfur on the periodic table, and so is chemically very similar. There may be a little more subtlety to it, but that's the main gist of it.Phenylethylamine wrote:They are modified amino acids called selenomethionine (MSE being the three-letter code they use for this particular modified residue). This means that the sulfur normally in the methionine residue has been replaced with a selenium atom.GCXC wrote:Hey, I'm just studying PARP-1 based off of 3OD8 and I see that they're a few ligands/amino acids (not sure what they are), but on proteopedia it calls them MSE can someone explain to me what exactly it is and if it has anything to do with the function of PARP...Thanks
They are not normally present in PARP; this is a modification that the crystallographers made so they could do some kind of imaging based on the position of the selenium atoms (I'm not sure why selenium, but this was in the original citation for 3OD8, albeit somewhat buried in the Materials and Methods section). So sadly, no, they are not relevant to the function of PARP; it's another one of those changes (like taking out some of the cysteines in caspase-3 in 1I3O) that the researchers made to make it easier to get the correct structure.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
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Re: Protein Modeling C
Just want to thank Phenyl and everyone else that contributed to this forum, without y'all I highly doubt I would've placed 2nd at State, our team came in fourth overall so two spots out from Nats (from TX), but since this is my senior year it was a good run
2012 State:
1st Robot Arm
2nd Protein Modeling
3rd Microbe Mission
1st Robot Arm
2nd Protein Modeling
3rd Microbe Mission
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