Hi I am using the latest build (1947 0.6 pre) of coot

Coot lsq superpose does exactly what I want it to do i.e superpose all the
atoms from one set of fragments to the ncs symmety other set of fragments.

Is it possible to have coot output to stdout  the transfomation matrix like
it does when it does a ssm match.

SSM superpose fails on this case since the superposed entities are still
poly-ALA . I have tried getting lsqkab from ccp4 to behave and do the same
thing but its quite tedious to  teach lsqkab which chains are related.

I know coot-lsq does the right thing , Is it possible for it to spit out the
transformation matrix for lsq as well  .

Thanks
hari

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