MichaelsSNoteBook/2008-4-18

04/18/08
Soo iterative rosetta design is running but takes a while.

In the meanwhile, Iam about to analyze the data a little bid more. I made the energy scatter plots today, looks pretty promising.

Stuff I need to do to analyze the data:

investigate following structure pairs

= rosetta design = 1J2A-1CLH    nomin    high energy NMR 1MG4-1UF0    nomin    X-ray higher energy 1UOH-1TR4    nomin    high energy x-ray > cutoff 1C44-1QND    nomin    high energy x-ray 1GNU-1KOT    nomin    high energy x-ray 1IFB-1AEL    nomin    high energy NMR 1BED-2IJY             high energy X-ray 1IFB-1AEL    E2_1000  NMR energy > cutoff

= SCADS = 1IFB-1AEL    nomin    nothing there 1J2A-1CLH    nomin    no NMR data

should investigate the rest to dobble check to. seems 1IFB-1AEL and 1J2A-1CLH are pretty bad structures.

=subset division = Additionally, I should divide my stuff into 4 groups. X-ray better before min NMR better before min

X-ray better after E2 100 NMR better after E2 100

perform for EACH structure pair! It's gonna help me to overlay subsets for every method, maybe I can identify subsets which have the same property for each method (would be awesome)

Check for differences and similarities: some ideas: Fold Sequence lenght rotamericity quality scores Joint RMSD, RMSD, epsilon, fraction core atoms aromatics (and other known issues)

thats it :)