Posts by Cory J. Russell

1) Message boards : Number crunching : Newbie Q&A, if you're new, have a view! (Message 48000)
Posted 24 Oct 2007 by Cory J. Russell
Post:
RMSD (Root Mean Square Deviation, IIRC) is used to compare the generated structure to the native structure (if the native structure is known). A score of 0 for RMSD would be an exact match. The accepted energy would be as low as possible with a score of 0 for RMSD.

So, for RMSD you would want to get as close to 0 as possible and the lower the accepted energy is, the better.

A RMSD score can only be calculated if the native structure is already known.


Greg, Transient, thank you very much for the responses, answers everything I needed!
2) Message boards : Number crunching : Newbie Q&A, if you're new, have a view! (Message 47929)
Posted 23 Oct 2007 by Cory J. Russell
Post:
Question regarding the RMSD and Accepted Energy. When getting to the native fold of the protein, is it better for these values to be closer to 0, or lower overall.

IE is RMSD better the closer it gets to 0? And is Accepted Energy better the closer it gets to 0, or the lower it gets overall? Just a few things I can't find an answer to being a newbie and all.

And as per Ben's post above...

"Can somebody please explain what keys on the keyboard change what about the graphics. I am interested in both a layman's and a scientific standpoint. I don't know why this info isn't in the graphics FAQ.

All I know is B and C do different stuff. Some of the numbers do the same. Please help."

I'd like to know as well, though only 'C' does anything for me in the view.






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