Dear Modeller Community,<br><br>I would like to ask how the unexpleained parameters affect the restraining process in restraints.make() and restraints.make_distance() commands<br>The manual is very good but I cannot see that this is fully explained. <br>
<br>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. <br>I thought of using sterics first, and then try distance restraints. For the distance restraints I thought of generating two &#39;same&#39; selections including CA atom of the <br>
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<br>homology model. How do you think that this sounds? Any other ideas for distance restraints? <br>
<br>FOR REFERENCE:<br>p.92<br><span class="gI"></span>make(atmsel, restraint type, spline on site, residue span range=(0, 99999),<br>residue span sign=True, restraint sel atoms=1, basis pdf weight=’LOCAL’,<br>basis relative weight=0.05, intersegment=True, dih lib only=False, spline dx=0.5,<br>
spline min points=5, spline range=4.0, mnch lib=1, accessibility type=8, surftyp=1, distngh=6.0,<br>aln=None, edat=None, io=None)<br>p.95<br>make distance(atmsel1, atmsel2, aln, spline on site, restraint group, maximal distance,<br>
residue span range=(0, 99999), residue span sign=True, distance rsr model=1,<br>basis pdf weight=’LOCAL’, basis relative weight=0.05, spline dx=0.5, spline min points=5,<br>spline range=4.0, accessibility type=8, restraint stdev=(0.1, 1.0), restraint stdev2=(0.0, 0.0,<br>
0.0), surftyp=1, distngh=6.0, edat=None, io=None, exclude distance=0.0)<br>