Discrepance between EOM and Crysol model dimentions

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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cesargandin
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Discrepance between EOM and Crysol model dimentions

#1 Post by cesargandin » 2019.01.09 14:52

Hello!

I'm using EOM to model a homodimeric protein with two intrinsic disordered regions. The models generated from EOM were apparently bigger than the dimensions o Rg and Dmax provided by the general algorithm. So, I used Crysol to simulate the scattering of the models generated by the EOM software and noticed a discrepancy between the values of Rg and Dmax obtained using the two softwares.
I also used the HYDROPRO software to compute the hydrodynamic properties of rigid macromolecules from their structure and the values obtained were in better concordance with the Crysol results.
Does EOM and Crysol programs uses different methodologies to calculate these structural parameters? Are the parameters obtained from the EOM reliable?
I'm using the latest version of ATSAS package.

Thanks in advance,

César A. Gandin.

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AL
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EOM uses CRYSOL to calculate the intensities

#2 Post by AL » 2019.01.28 19:54

cesargandin wrote:
2019.01.09 14:52
So, I used Crysol to simulate the scattering of the models generated by the EOM software and noticed a discrepancy between the values of Rg and Dmax obtained using the two softwares.
What was the difference? 1%? 10%? What values from the CRYSOL log did you use as Rg and Dmax? (Should be "Rg from the slope of net intensity" and "Envelope diameter".)
cesargandin wrote:
2019.01.09 14:52
Does EOM and Crysol programs uses different methodologies to calculate these structural parameters?
EOM uses CRYSOL to calculate the intensities. Make sure you use the same settings (Number of harmonics, Maximum s value, Number of points) when running EOM and CRYSOL.

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