Re: [COOT] [ccp4bb] superpose structures .ssm or lsq which is better

[Paul Emsley]

junfeng liu wrote:
Dear All,
I am overlaying several structures using coot. There are two ways SSM 
or LSQ can be used  in that package.  But I got clearly different  
result  form  the two methods. In my opinion SSM only works on the 
secondary structures and LSQ can works on the whole atoms ,main chain 
or CA.
So the question is which one is better to overlay structures, LSQ or 
SSM ?

Dear Liu,

Depends on what you are trying to do.  If you are trying to overlay 
proteins that are homologous but have low sequence identity, then 
finding which atoms/residues match with which can be pretty difficult - 
hence you would use SSM.  If, however, your protein chains are similar 
(for example, because they are NCS-related perhaps) then LSQ over a 
particular residue range is probably a better option.

Paul.