Folding Molecule Visuals/Graphics - what are they?

[audifan]

Hi,

Sorry if this has been asked before - does anybody know what the molecule visuals/graphics actually represent - is this just eye candy or do they relate in some way to the *actual* calculation being performed at the time by the folding client (I am running a PS3) ?

Thanks,
Mark

[bruce]

Hi,

Sorry if this has been asked before - does anybody know what the molecule visuals/graphics actually represent - is this just eye candy or do they relate in some way to the *actual* calculation being performed at the time by the folding client (I am running a PS3) ?

Thanks,
Mark

While it does provide some nice eye-candy, the molecule that the PS3 displays is a real-time display of the computations which are being performed. This is a very significant improvement over the PC clients which display static images of the current protein.

If you're interested in some of the other proteins that FAH has folded, many of the static images have been collected by a 3rd party at http://jmol.sourceforge.net/fah/

[njdcampbell]

Hi,

Apologies if this is somewhere in the FAQs, but I've looked and can't find the answer. In the graphical representations (I'm using ball-and-stick) what do each of the various colours represent? Are they individual atoms or sub-structures of some sort? In either case, is there a key for the colours?

Thanks,

Nick

[toTOW]

Each color reprents an atom type (black = carbon, red = oxygen, orange = sulfur, white = hydrogen, blue = nitrogen, ...).

[njdcampbell]

Thanks toTOW.

Do you know if there is a full key somewhere on the FAH website? Or is this a standard colour coding, in which case if you could point me to a resource that detailed it, I'd be grateful.

Cheers,

Nick

[NicoV]

For Jmol, you have http://jmol.sourceforge.net/jscolors/

[Ivoshiee]

http://folding.stanford.edu/English/FAQ-main#ntoc61:

There are currently two visualization modes: Space-filling and ball-and-stick. In ball-and-stick mode, each small ball represents an atom, and the sticks represent bonds between atoms. In the space-filling model, each filled sphere represents the approximate volume that the electrons occupy around each atom. In both modes, carbon atoms are drawn in dark gray, hydrogen atoms are drawn in light gray (although some hydrogen atoms are not drawn at all), oxygen atoms are drawn in red, nitrogen atoms are drawn in blue, and sulfur atoms are drawn in yellow.

[njdcampbell]

Thanks Ivoshiee, I knew it had to be there somewhere, although I admit I didn't look for something buried that deep under Windows / OSX. Also, unfortunately, that doesn't seem to be an exhaustive list or quite right for the PS3 (hydrogen seems to be pale blue).

Perhaps it is the Jmol convention (thank you NicoV) with hydrogen as pale blue in place of helium?

Maybe, given that the PS3 representations are so much more sophisticated than for the other OS, someone associated with the site could add a specific FAQ in that section.

Thanks again for your responses,

Nick