Oligomer and RNA

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)
Post Reply
Message
Author
jans
Guest
Posts: 2
Joined: 2019.08.10 22:35

Oligomer and RNA

#1 Post by jans » 2020.07.22 14:41

Hi,
I have a mixture of several components, part is protein, part RNA, and potentially complexes. For some of the individual components I have SAXS data, for some I have potential PDB model.
Is there anything to consider when running Oligomer regarding RNA? Like different scattering power/electronic contrast between peptides and (R)NA?
Jan
P.S. Without any considerations I am getting chi2=8ish

konarev
Administrator
Posts: 54
Joined: 2007.09.14 15:38

Re: Oligomer and RNA

#2 Post by konarev » 2020.08.24 14:30

Hi Jan,
in the case of protein-RNA mixture, one needs to create the form-factor file using FFMAKER (for PDB models),
it will contain in its header the information about electron density contrasts of the components.
OLIGOMER will take it into account by normalizing the volume fractions of the corresponding components.

jans
Guest
Posts: 2
Joined: 2019.08.10 22:35

Re: Oligomer and RNA

#3 Post by jans » 2020.09.17 13:35

Thank you very much for the reply.
When the RNA is as measured data, oligomer should be fine to, right?
We had to remeasure anyway, because it turned out there were some issues with the sample, after we are getting chi2 below 2. I am just not sure, how much should be addressed to noisy data of one of the components...
Jan

konarev
Administrator
Posts: 54
Joined: 2007.09.14 15:38

Re: Oligomer and RNA

#4 Post by konarev » 2020.09.23 16:26

If for RNA only experimental curve is available, one can use it as well.
It needs to be properly normalized (compared to the theoretical curve from the protein),
and the information about the contrasts should be present in the header of the form-factor file.

Post Reply