Re: [modeller_usage] using DSS/BS crosslink information as restrain

[thereal sisterdot <>]

Hey all,

I decided to try using upper_bound restraints as above to feed the crosslink information to modeller.

But actually the restraints did not improve the conflicting distances.

my assumption is that the few restrains from the crosslinks can not compete with the many restrains coming from the alignment.

I guess one would have to modify the model later somehow.

maybe using imp?

greets

Maria

On Mon, Sep 7, 2015 at 11:19 AM, thereal sisterdot <" target="_blank">> wrote:

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