SASREF for large RNA

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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ibelalov
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Posts: 11
Joined: 2013.12.18 05:00

SASREF for large RNA

#1 Post by ibelalov » 2015.02.03 22:28

Dear SAXS people,

I have a curve from 210 nucleotides RNA. DAMMIF gave descent shapes even for the entire curve without any datapoints removed. For the curves without low/high angles data points fits were even better, both in terms of chi and the actual fit for the curves. Shapes were looking more or less like they were expected to.

However SASREF fits look awful, with chi values higher than 15 for processed curves, and (what is weird too) ~8 for the raw data.

I've built 7 fragments with MC-SYM, and submitted them with contact points and distance 3.4 A (distance between nucleobases in an RNA A-helix).

Is there something I am missing? Maybe there are some requirements for the PDB atom names or something else.
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sasref_fit.png
SASREF fit for the processed curve
sasref_fit.png (5 KiB) Viewed 3982 times

ibelalov
Member
Posts: 11
Joined: 2013.12.18 05:00

Re: SASREF for large RNA

#2 Post by ibelalov » 2015.02.05 01:55

The issue was solved with providing more accurate contact information. If the RNA fragments looks like:
5'-residues 1 to 21-3' + 5'- residues 22 to 45-3'
3'-residues 90 to 70-5' + 3'-residues 69 to 46-5'

contacts should be provided the following way:
fragment1.pdb from residue 21 to residue 21 fragment2.pdb from residue 22 to residue 22
fragment1.pdb from residue 70 to residue 70 fragment2.pdb from residue 69 to residue 69

instead of (what I did the first time):
fragment1.pdb from residue 21 to residue 70 fragment2.pdb from residue 22 to residue 69

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