Describing sidechains in the graphics

Message boards : RALPH@home bug list : Describing sidechains in the graphics

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Message 2328 - Posted: 6 Oct 2006, 21:18:27 UTC

Here is Chu\'s initial description, let\'s see if we can beef it up a bit and create a description for when this is released on Rosetta which will help people understand what\'s happening, what differences they will observe in the running of WUs etc.


What are side chains?
For general knowledge about protein and amino acid, please visit here. I notice that some key terms like \"sidechains\" are missing and we will update that soon. Here is something I wrote quickly and it definitely needs to be improved.
20 natural amino acids have part of their structures in common and they are connected via peptide-bond linkages to form the topology of a protein structure. The common part is called \"backbone\". Amino acids differ from each other by its unique chemical group which connects to the C-alpha atom of the backbone and that group is called \"side chain\".

Why do they blink on and off?
Sidechains are part of protein structures but we only choose to show them on screen during some certain stages when they are being changed by the program.

Why can\'t I see side chains in the other boxes? Mine must be broken.
So far we only enable the sidechain drawing for the \"searching\" box.

Are we doing calculations differently now on the side chains? Or simply illustraiting the calculations we\'ve been doing all along?
Sidechain calculation has been part of Rosetta program for a long time, but we only start to have them illustrated on the screen recently.

I understand the above is still far from an adequate description. But I will try my best to provide more information on future updates and this will give people like you guys who volunteer to help testing a better chance to send us feedbacks. Many thanks again.


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Message 2359 - Posted: 8 Oct 2006, 20:25:29 UTC

I\'m thinking something like this:

Prior versions of Rosetta@Home presented only the backbone of the protein being examined in the graphic display. Now, we\'ve added support to display more details of the modelled protein. The graphic will now show the sidechains in the searching box when the model reaches a point where the sidechains are being optimized. This is generally the phase when the shape shown in the graphic just seems to twitch and jitter and not really move. Now, with the sidechain detail shown, you can see in the graphic how the sidechains may effect the overall structure of the protein.

This sidechain optimization is what occurs in the \"full atom relax\" stage of the model. These are calculations we\'ve been performing all along, but now with the graphic enhancements, you can see them illustraited and hopefully you can better understand how your computer is helping Rosetta@Home to study proteins.
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Message boards : RALPH@home bug list : Describing sidechains in the graphics



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