Just noticed when the screen saver kicked in...there doesn't seem to be a NATIVE structure that is being aimed at and the RMSD never leaves the left hand edge of the panel on the top right of the screen saver screen.

Is this a problem with the WU or the screen saver ?

Cheers

PS Sorry if this is in the wrong forum

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Just noticed when the screen saver kicked in...there doesn't seem to be a NATIVE structure that is being aimed at and the RMSD never leaves the left hand edge of the panel on the top right of the screen saver screen.

Is this a problem with the WU or the screen saver ?

There are several types of proteins in the queue that don't have a native structure (can't remember their names). I don't think it's an error maybe it's a part of what David Baker announced here

https://boinc.bakerlab.org/rosetta/rah_medical_relevance.php

Maybe a project admin could clarify this in a short sentence.

Maybe a project admin could clarify this in a short sentence.

I think some WUs went out without the native structure included, even though it is a protein with a known native structure. Should be fixed soon.

I should point out that this does not effect the results. The native is only there as a reference and is not used during the calculations.

Thanks very much for the clarification

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Maybe a project admin could clarify this in a short sentence.

I think some WUs went out without the native structure included, even though it is a protein with a known native structure. Should be fixed soon.

I should point out that this does not effect the results. The native is only there as a reference and is not used during the calculations.

Thank you very much! This is what makes rosetta unique compared to other projects: immediate response to the crunchers.

Shouldn't the native structure be included to calculate the RMSD?

"RMSD" shows how close the currently accepted structure is to the right answer. (x-axis is RMSD, y-axis is progress.)

The right answer is the native structure right?

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Proud member of the Dutch Power Cows

Shouldn't the native structure be included to calculate the RMSD?

"RMSD" shows how close the currently accepted structure is to the right answer. (x-axis is RMSD, y-axis is progress.)

The right answer is the native structure right?

You are correct about this. And for the current phase, where we're testing and refining the algorithm, having the native structure and hence the RMSD is very useful.

However, when we go "live" we will be working on proteins whose native structure is not known, because our job will to be to try to find that native structure. In cases like this, we can't possibly know what the RMSD will be.

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Shouldn't the native structure be included to calculate the RMSD?

"RMSD" shows how close the currently accepted structure is to the right answer. (x-axis is RMSD, y-axis is progress.)

The right answer is the native structure right?

Yes, the right answer is the native. The native structure should be included to calculate the RMSD. However, we can always calculate the RMSD after the fact. After WUs send the final models back to our server we can then calculate their RMSD from the native. It is more convenient to have it done in the WU, and more interesting visually.