I am experiencing some discrepancies between OLIGOMER and other programs from ATSAS, in particular with SASREFMX and CRYSOL.
First case: I have a mixture of monomer and dimer and used SASREFMX to model the dimer. The obtained model has quite good fit to experimental data. But when I am running OLIGOMER using as input files the dimer model from SASREFMX and the monomer (that I provided as an input to SASREFMX), the fit is much worse.
Second case: due to the previously mentioned problem, I decided to use OLIGOMER for the monomer only. I have a crystal structure (.pdb) and experimental data where I have only the monomer. Using CRYSOL, I am getting a good fit between SAXS and pdb file.However, when I run OLIGOMER using monomer.pdb as the only component for ffmaker, it does not fit to an experimental data anymore (with or without subtraction of constant).
Did any one experienced similar problem? How can I fix it? I would like to calculate how the amount of dimer changes with concentration, but since both monomer and dimer have worse fit in OLIGOMER (then in CRYSOL and SASREFMX), it is not possible.
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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