I would like to ask how the unexpleained parameters affect the restraining process in restraints.make() and restraints.make_distance() commands

The manual is very good but I cannot see that this is fully explained.

Also, as a person who is using MODELLER homology modelling the first time, I would like to ask what types of restraints I should use at the beginning.

I thought of using sterics first, and then try distance restraints. For the distance restraints I thought of generating two 'same' selections including CA atom of the

first, middle and the last residues within each secondary structure. Then one can use both of these two selections to generate a ( n x n ) distance matrix to train the

homology model. How do you think that this sounds? Any other ideas for distance restraints?

FOR REFERENCE:

p.92

make(atmsel, restraint type, spline on site, residue span range=(0, 99999),

residue span sign=True, restraint sel atoms=1, basis pdf weight=’LOCAL’,

basis relative weight=0.05, intersegment=True, dih lib only=False, spline dx=0.5,

spline min points=5, spline range=4.0, mnch lib=1, accessibility type=8, surftyp=1, distngh=6.0,

aln=None, edat=None, io=None)

p.95

make distance(atmsel1, atmsel2, aln, spline on site, restraint group, maximal distance,

residue span range=(0, 99999), residue span sign=True, distance rsr model=1,

basis pdf weight=’LOCAL’, basis relative weight=0.05, spline dx=0.5, spline min points=5,

spline range=4.0, accessibility type=8, restraint stdev=(0.1, 1.0), restraint stdev2=(0.0, 0.0,

0.0), surftyp=1, distngh=6.0, edat=None, io=None, exclude distance=0.0)