Hi,
I'm modelling a GPCR based on rhodopsin as a template. The
sequence similarity is relatively low (<20%), but the conserved
residues are located in the 7 Transmembrane
Helices, and the alignment of the TMs is obvious. It is assumed
that the topology is well conserved (more so than expected from
the sequence similarity), because of the known folding pattern in
the GPCR-family.
The question is this:
Is there any way to assign greater weight to the conserved
residues in the TM-regions in the distance constraints in the pdf,
or in any other way assure that the information about the
conserved residues won't get lost in the optimization?

Thanks,
Dan

--
Dan Thomas Major (at Dr. B. Fischer's lab)
Bar-Ilan University
Ramat-Gan, Israel