[modeller_usage] using DSS/BS crosslink information as restrain

[thereal sisterdot <>]

Dear modeller users and "caretakers",

i was using modeller to model a heterohexameric complex from mouse where the yeast orthologous structure is known.

to evaluate the models i used the DOPE score and visualized a dozen available intersubunit DSS/BS crosslinks using Xlink Analyzer in chimera.
 

for 2 neighbouring subunit 3 crosslinks indicate that the published heterohexameric complex appears to have a different arrangement in that part than the published one (crosslinked residues between subunits are around 60A apart)

in order to obtain a model satisfying those crosslink restrains would one add the 3 crosslinks as below, or can you recommend a better approach:

class MyModel(automodel):
  def special_restraints(self, aln):     
     rsr = self.restraints 
     at = self.atoms

# Constrain the distance between alpha carbons in residues 611 chain D
# and 224 chain B to be less than 30 angstroms:
rsr.add(forms.upper_bound(group=physical.xy_distance,
                          feature=features.distance(a['CA:611:D'], a['CA:224:B']),
                          mean=30., stdev=0.1))

thanks a lot!!!!

Maria