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