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World Community Grid Forums
Category: Retired Forums
Forum: Member-to-Member Support [Read Only]
Thread: Is the Rosetta 3D protein graphic canned or real? |
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Thread Status: Active Total posts in this thread: 12
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I think the 3D rotating graphic of the "current protein" is NOT really the one currently being worked on. The graphic is the same as it was weeks ago, and it goes through the same steps and "flips" every time. My PC has returned many results so far, so I know the graphic should change.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
My comments may have been about the version of Rosetta running before yesterday's update. The graphic still looks strange to me ... an unchanging object rotating in 3d for a few seconds, then a very different static object rotating, then another, etc. Last week the graphic always started with the same stretched-out figure and then had the same changes following. Question: For a PC running a single calculation, is the "movie" or sequence of graphics likely to be the same every time? Answer this for the version before yesterday and the one running now. Thx.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
The protein graphic has not been changed. At intervals, a snapshot is taken of the current sequence being folded. It is converted into a 3D graphic diagram, then displayed. The diagram is then rotated in steps on the screen to show the 3D complexity. A new function added to the routine slows down the rotation on a slow computer, to minimize CPU overhead. It is real, not canned. Of course, it is a single snapshot and does not follow all the changes being computed on your computer. Eventually another snapshot is taken.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
As posted by Rick before
The protein that you see displayed is a snapshot of the current protein as it's being folded, rendered using OpenGL. We could show the folding in close to real-time, but there are two problems with that: First, all your computing power would be wasted drawing it. Second, the protein would be jumping all over the place and would look very erratic. Instead, we take a snapshot of the protein at semi-random intervals so as not to waste much CPU time on the graphics. Everytime the graph begins we're starting from basically a raw sequence of residues. As the graphs progress the protein becomes more folded. You may have noticed that if the protein is updated (not just rotated) when the graphs have just started, it might look like a rather long line of residues. Likewise, if it is updated near the end of the graph it will most likely look folded up into a ball. If you want to see a video of Rosetta folding a protein, check out the movie on the Institue for Systems Biology page for this project: http://systemsbiology.org/Default.aspx?pagename=humanproteome |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Yep. That was a response I had on my post. I never could find the movie in reference.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Here is the movie, toward the bottom of the Human Proteome page:
"For a quicktime movie showing a protein (Ubiquitin) being folded by Rosetta click here [1d3z.mov OR 1d3z.mpg ] " It takes a couple of minutes to download, and you have to move the cursor to the bottom to have it suddenly turn into an hour-glass, showing that something is going on while staring at a blank screen. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
That protein folding video doean't look anything like the picture of the protein my computer is working on.
 Hmmm |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Stokes --
They do not look the same because differing methods of representing the chains of molecules are used. In the movie, they are represented by stick figures and in the view we get from the WCG agent, individual molecules are represented by colored balls. I do not know this for a fact, but I would presume that the different colors in the stick animation in the movie from the ISB site would represent specific chains of molecules. Perhaps mycrofth, another of the Community Admins who is much more familiar with the folding processes, might care to respond to this. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I may be misunderstanding what I have read, but here goes. Rosetta has a low resolution and a high resolution method of folding proteins. We are currently using the low resolution folding method, for speed. We have tables listing the angles that chains 3 - 9 amino acids long can take when folding. So we split up a protein into components corresponding to chains of amino acids in our table and start calculating force vectors and then choose to fold a component in the particular angle in the table that the overall force vector at that point seems to indicate. Using a table like this reduces the computation needed by orders of magnitude over what we would need if we tried to deal with each individual atom.
The question remains, is each colored ball in the diagram an individual amino acid or not? I believe that each colored ball in the diagram corresponds to a component. The size of the ball displayed corresponds to the number of amino acids in that component. But I am guessing that because the balls seem to vary a great deal in size. If it were not for the apparent size difference, I would just assume that each ball represented one amino acid. Keep in mind, this is just my guess, and I may be misinforming you.  mycrofth |
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