MichaelsSNoteBook/2008-4-18: Difference between revisions
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= SCADS = | = 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. | 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. | 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) | 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) | ||
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Check for differences and similarities: | Check for differences and similarities: | ||
some ideas: | some ideas: | ||
Fold | |||
Sequence lenght | |||
rotamericity | |||
quality scores | |||
Joint RMSD, RMSD, epsilon, fraction core atoms | |||
aromatics (and other known issues) | |||
thats it :) | thats it :) | ||
Latest revision as of 15:58, 18 April 2008
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 :)
