[modeller_usage] Special distance restraints weighting

Hello everyone,

I would like to know if there is a possibility to force Modeller to use a certain

distance in a model, even if that means distorting the template by a great

value? I am using user distance restraints as shown in Modeller's manual.

I am trying to build a model of a protein where the distance between two

loops is 20 Angstroms bigger than in the template - problem is, the models

would not adopt the given distance, but would stick more or less to the

conformation of the template structure as the sequence identity is very high.

I presume this high sequence identity results in a strong contribution to the

molecular pdf, and this prevents the loops to modelled in the requested

conformation.

Does anyone know how to solve this problem?

Thorsten Schweikardt

Molecular Biophysics

University of Mainz