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.
- Re: [COOT] [ccp4bb] superpose structures .ssm or lsq which is... Paul Emsley
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