Hi,
I manually modeled a protein-RNA complex which I am confident that it is
basically right. This protein has two domains which bind different sites
of a RNA. One of the domain has a ligand and one atom of the ligand has
a constant distance with a specific base of the RNA. Now I want to
refine this model but there are some constraints must be concerned.
First the relative position of the two domain can be adjusted that is
the linker between the domain can be flexible. Second, the sidechains in
the protein-RNA interface can be refined but for the rest of the domain
and ligand i just want to do rigid-body refinement. And last the
distance between the two atoms of protein and rna must be restrained in
2A. So here is my quension: can Xplor-nih do this work for me? if can,
which script should i use and how to define these constraints.
I appreciate any help on my question!
