What do the colours represent?

[stevebarnes15]

Hi guys just a quick post.

Curious to know what the colours mean,on the folding display,have googled,but not being a quantum physisist or whatever you may call them,i find it a bit hard to compute.

Why is that one green whilst others are blue/red/grey?

 

[yuri04]

You are looking at the model of a folding protein, and the atoms and there connections.

Not sure what the light blue is, as there is no description of it, but if I had to venture a guess I think it's Fluorine. not sure what that's based on, perhaps because of my toothpaste

To see what the other are:

http://folding.stanford.edu/English/FAQ-main#ntoc64

We might be able to figure it out by the project description, so if you give us the project number we can see if it's in the description.

 

[stevebarnes15]

Work Unit is Gromacs

It's project number 10437(Run 1398.Clone 0,Gen 8).Core a4

and the green atom doesn't seem to be connected to any other atom,and is solitary.

 

[yuri04]

http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=10437

mmm, doesn't really help

http://folding.typepad.com/news/2007/09/how-fah-works-m.html

that might explain it, it could be a lipid vesicle.

which also explaines why it isn't attached to the molecule itself. However it could also be that in this state of the Project the molecule just hasn't been connected yet.

As every WU is only a very small part of the entire folding process (like one frame in an entire movie).

or even that in this model the connection just is not showed.

 

[Firat]

Ooo some biochemistry,

Well red = oxygen

Blue = nitrogen

Darker and slightly bigger Grey in this case I'm assuming should be = carbon

The smaller lighter grey molecules = hydrogen

Look carefully there are 2 grey types if molecules

And that odd cyan molecule should be sulfur

And that's all

 

[yuri04]

The cyan (Tnx, I was looking for that

) isn't sulfur, as sulfur is yellow.

Sulfur was btw also my first guess, but according to the FAQ sulfur shows up as yellow.

 

[Firat]

Yh I kno but carbon should also be black and hydrogen should be White....

So there is a colour mix up here already

Apart from nitrogen, oxygen, carbon, hydrogen and sulphur no other molecule contributes to a protein as there is no amino acids containing any other molecule other then the ones I've mentioned so it has to be sulphur

 

[yuri04]

I agree, however according to the Stanford FAQ, they don't comply with the 'regular colors'.

so yeah it could be sulfur, but as folding has evolved from the regular proteins to more complex systems with more and more molecules. It could also be something else.

I think the only way to figure this out right is to email Dr. Pande or the guy who runs the Project 10437.

 

[Firat]

I see what you are saying but protein can only consist with the 5 molecules I've pointed out, just with different arrangements, orientations and amino acids between residues. They are very complex as they can have a number of amino acids but I'm not aware of any other modification that involves other molecules,

I'll ask my amino acid professor just to be sure when I see him next

 

[Firat]

Ahhh just remembered , proteins can me modified on specific residues they can be phosphorylated = phosphate molecule, methylated = carbon + 3 * Hydrogen and acetylated = carbon + oxygen + carbon + hydrogen * 3

 

[stevebarnes15]

thanks for the input guys,if all else fails we'll have to send it to myth busters.lol

 

[Firat]

So mayb it's a phosphate ???

 

[yuri04]

Well as it's a model it does not even have to be just one molecule. It could very well be a something like a transport vesicles, I mean in a model they can let something represent whatever they want.

Although a transport vesicles might not be the best example sizewise

I'll see if I can email the man who runs the project.

ow Steve what have you done

Edit: ow, just missed some posts there, but yeah that is a very plausable explanation, we are now starting to go into the grey area's of my memory

 

[Firat]

Ahhhh who cares as long as it helps to save lives, if you email the guy he's probs too busy to tell you what molecule it is, let's call it molecule x

Let's fold away

First I need to rebuild my rig though :/

 

[stevebarnes15]

Sorry my bad,but curiosity killed the cat ya know

I've only been folding around a month so was just looking at it in a bit more depth to try and get an understanding of it.

I can garuntee we'll all learn something now.

 

[yuri04]

ah well

can't fault you for trying to learn something right

So, I emailed Kyle, the manager of the 10437 Project.

and he replied by posting in the folding forum itself as well as answering my email:

Hi,

I think that is a chloride ion. I made a post here:

http://foldingforum.org/viewtopic.php?f=24&t=17841

and also provided a link to wikipedia:

http://en.wikipedia.org/wiki/Guanidinium_chloride

Best,

Kyle

so yeah, we were close

well kinda

And a thanks to Kyle Beauchamp for the support and quick respons in this matter.

 

[stevebarnes15]

ah nice one!,well i guess that solves the puzzle.