Hello all!<br><br>I&#39;m new at Modeller and I&#39;m trying my luck with Distance Restraints to model a small domain of a protein. I was running some tests on my modelling to see if I had those restraints working and, from my preliminary (and rookie) analysis, it seems it&#39;s not.<br>
<br>Attached are the files I&#39;m using. The MyModel.py script has the MyModel class with my restraints defined. It is then called by the main modeller script (RNF11_1X4J_rest.pdb) (had to use this approach for parallel computation) which runs on modeller 9v5.<br>
<br>I&#39;ve described each restraint like this:<br><br><span style="font-family: courier new,monospace;">rsr.make_distance(at[&#39;SG:1&#39;],at[&#39;SG:4&#39;],aln,spline_on_site=False,restraint_group=physical.xy_distance,maximal_distance=5)</span><br>
<br>I just want both atoms to be, in a maximal distance of 5A. I made some further tests with that value of maximal_distance at 1.5 and 0.5, just to see if it ran ok, and I found out that the 3 best models (5A, 1.5A, 0.5A) are exactly the same :x (or nearly), with distances in the order of 2-3A, which would violate this restraint I&#39;ve added in the 1.5A and 0.5A.<br>
<br>Is this behaviour normal, or is it something I&#39;m doing that is not the most correct?<br><br>Thanks in advance for the answers and congrats for the software and for the whole team.<br clear="all"><br>João Rodrigues<br>
Bijvoet Center for Biomolecular Research<br>Utrecht, Netherlands<br>