Hi,

The low RMSD between model and template is expected when you are using a single template, even at low sequence identity, the model does not have much of a choice but to follow the template. How low is the target-template sequence identity in this case?. The many bad contacts may be a consequence of misalignments rather than large structural differences between target and template. If the sequence identity is sufficiently low (<30%) alignment errors become more and more of an influence on the accuracy of the model. You may want to try some alternative alignments (maybe some profile-based alignment) and see if the bad contacts dissappear.

I hope this helps.

Best,

Roberto

-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/

> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org]On Behalf Of Margot > Ernst > Sent: Thursday, December 05, 2002 4:57 AM > To: modeller_usage@salilab.org > Subject: low sequence identity > > > Dear Modeller support, > I am modeling at low sequence identity and I believe to have the > following > problem: The homologous scaffold (comprising a core of beta > strands) of my > target, after a fisrt round of modeling, displays a > (suspiciously) low RMSD > with respect to the template, and a LOT of bad contacts involving the > hydrophobic core. Consequently I think that in my target > secondary structure > motifs should be arranged more spaciously. How can I accomplish > this in terms > of additional modeling restraints, or chopping up the alignment > and modeling > in pieces, or whatever will work? > thanks, > margot > > >