curve fit for protein-RNA complex

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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bear
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curve fit for protein-RNA complex

#1 Post by bear » 2016.09.02 12:49

Hi,

I can nicely build a 1:1 protein:RNA model in MONSA, which takes into account the different scattering power. Now the question is, do the other programs (CRYSOL, SASREF, CORAL, ...) automatically or otherwise understand that the PDB file contains both protein and RNA and correct for it?

While this is of interest also otherwise, of course the spark for this question comes from a referee comment, not happy with all curves fitting well in MONSA...I mean I can run SASREF or jsut superpose the individual crystal structures on the MONSA model, but is the fit calculated from these correct?

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AL
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Re: curve fit for protein-RNA complex

#2 Post by AL » 2016.09.02 16:50

bear wrote:Now the question is, do the other programs (CRYSOL, SASREF, CORAL, ...) automatically or otherwise understand that the PDB file contains both protein and RNA and correct for it?
Yes, they do.
bear wrote:While this is of interest also otherwise, of course the spark for this question comes from a referee comment, not happy with all curves fitting well in MONSA...I mean I can run SASREF or jsut superpose the individual crystal structures on the MONSA model, but is the fit calculated from these correct?
I'd recommend to run SASREF. It will compute the scattering taking the actual atoms into account.

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