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