My question is dealing with the number that is found on each WU. I've noticed that the lower the number (T30*, T29*, etc) that I'm more apt to produce a segment with both the RMSD and Accepted Energy graphs. The higher the number (T38* and so forth) only produce the Accepted Energy graph on the screensaver.

Is there a reason why this is? Or is this a random act that 'pops' up? Thanks for your assistance.

---

The current WUs are numbers as based upon the CASP study proteins... none of which had a known structure... when CASP started anyway. Now that the main phase of CASP has passed, we're seeing WUs with the word "FOLLOWUP" in their names. These are running on some of the first CASP proteins which were released several months ago, and NOW have a known structure.

The RMSD figure is a measure of how close your current prediction is as compared to the known structure of the protein.

My best guess is that the Baker team was very challenged by some of these proteins and so now they are looking at them again and working to learn how they could have made a better prediction then the one they came up with. This is how the science progresses. And so they are trying a new approach or running additional trials against these proteins and will learn more about how to make accurate predictions of similar proteins in the future.

So, when the 3D structure of the protein is known, the graphic is displayed differently then what we've been crunching all Summer with the unknown CASP proteins.

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

The structure of the lower numbers has been released and what you're currently predicting can be compared to the real structure (that's what RMSD does)

The T80* haven't been released, so there's nothing to compare it to.

---

Thank you, Gentlemen. A little more knowledge to store in the back of my brain. LOL :)

---

I should have pointed out, since the structure is known, you see a box in the graphic which does not change labeled "native structure". THIS is what you want your predicted structure ("Low energy") above it to look like. Sometimes it's hard to tell how close you are because your prediction seems to be spun around the other way... so you can mouse over and drag the native structure to rotate it along any axis to try and size up how it looks as compared to your prediction. You can also right click and drag up and down to zoom it in and out.... can't WAIT for them to add the side chains in the graphic too. That will be fun to zoom! Have fun!

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

Okay, here's another curveball. hehehe The latest WU has a little red dot in the lower corner (graph) where the RMSD and Accepted Energy lines cross. Does this denote the lowest RMSD and Accepted Energy that was found? Or what the computer is shooting for during this session?

I'm a bucket of questions, just trying to 'spill' out a few at a time. LOL

---

The red dot indicates one of your own prior predictions for this protein. The longer you crunch this WU (see WU runtime preferences), the more models you will complete. Once your current model ventures in to the energy levels of your prior predictions (i.e. once the scale on the screen becomes appropriate) you will see a red dot for each prior prediction which is within that same scale. I mean you rarely see ALL of your prior predictions on the screen, because some are above or below the current energy scale of your present model.

By the way, the ideal RSMD, i.e. the perfect match to the native structure would be a 1.0

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

By the way, the ideal RSMD, i.e. the perfect match to the native structure would be a 1.0

Hi Feet1st,

that is not correct. The RMSD is measured in Angstroms (i.e. 10^-10m or 0.1 nm) and the perfect match is 0,0 (you can see that on the Top Predictions Page where the scale always runs down to 0. The below image from that page demonstrates that: the RMSD of the best predictions is clearly lower than 1.

---

"I know that you believe you understand what you think I said, but I'm not sure you realize that what you heard is not what I meant." R.M. Nixon

Oh thanks for that. I can never remember (because I don't fully undertand) if it's 1 or 0... either way 1.0 is pretty good ;)

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

Oh thanks for that. I can never remember (because I don't fully undertand) if it's 1 or 0... either way 1.0 is pretty good ;)

The way I remember it....RMSD=Root Mean Square Deviation (or sometimes Distance or Difference)...

The "smallest" possible difference (or distance) is always going to be 0 -- or "the same".

I found a pretty good explaination of it here