MichaelsSNoteBook/2008-4-18

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(rosetta design)
Current revision (18:58, 18 April 2008) (view source)
(SCADS)
 
Line 21: Line 21:
= SCADS =  
= SCADS =  
-
1. 1IFB-1AEL    nomin    nothing there
+
1IFB-1AEL    nomin    nothing there
-
2. 1J2A-1CLH    nomin    no NMR data
+
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.  
-
1. X-ray better before min
+
X-ray better before min
-
2. NMR better before min
+
NMR better before min
-
3. X-ray better after E2 100
+
X-ray better after E2 100
-
4. NMR 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)
Line 38: Line 39:
Check for differences and similarities:
Check for differences and similarities:
some ideas:
some ideas:
-
1. Fold
+
Fold
-
2. Sequence lenght
+
Sequence lenght
-
3. rotamericity
+
rotamericity
-
4. quality scores
+
quality scores
-
5. Joint RMSD, RMSD, epsilon, fraction core atoms
+
Joint RMSD, RMSD, epsilon, fraction core atoms
-
6. aromatics (and other known issues)
+
aromatics (and other known issues)
thats it :)
thats it :)

Current revision

Contents

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 :)

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