Hello all!
I'm new at Modeller and I'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's not.
Attached are the files I'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.
I've described each restraint like this:
rsr.make_distance(at['SG:1'],at['SG:4'],aln,spline_on_site=False,restraint_group=physical.xy_distance,maximal_distance=5)
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've added in the 1.5A and 0.5A.
Is this behaviour normal, or is it something I'm doing that is not the most correct?
Thanks in advance for the answers and congrats for the software and for the whole team.
João Rodrigues Bijvoet Center for Biomolecular Research Utrecht, Netherlands