[ccp4bb] how to overlap DNA

[Junfeng Liu]

 Dear All,
  Does anybody has the experience to overlap DNA in the  protein
complex? I have tried the LSQ in Coot and it works ok but  not
perfectly. Could you please tell me a better way to do that?Or can
Coot be used to overlap  DNA/RNA on their  back bone  by LSQ or SSM ?
At   the same time, are there some software or servers can be used to
 search the "homology DNA " in the database like the Dali on
protein?
  Thanks in advance!
  Best wishes
  leo