  Background. All-atom crystallographic refinement of proteins is a laborious
manually driven procedure, as a result of which, alternative and multiconformer
interpretations are not routinely investigated.
  Results. We describe efficient loop sampling procedures in Rappertk and
demonstrate that single loops in proteins can be automatically and accurately
modelled with few positional restraints. Loops constructed with a composite
CNS/Rappertk protocol consistently have better Rfree than those with CNS alone.
This approach is extended to a more realistic scenario where there are often
large positional uncertainties in loops along with small imperfections in the
secondary structural framework. Both ensemble and collection methods are used
to estimate the structural heterogeneity of loop regions.
  Conclusion. Apart from benchmarking Rappertk for the all-atom protein
refinement task, this work also demonstrates its utility in both aspects of
loop modelling - building a single conformer and estimating structural
heterogeneity the loops can exhibit.
