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Dear Xiao Lei, In my opinion, lsqman from the Uppsala Software Factory is the most flexible program for aligning structures. Aligning based on dsDNA should also be possible in lsqkap, I guess. Best, Tim On Saturday, May 13, 2017 1:29:27 PM CEST Xiao Lei wrote: > Dear All, > > I was wondering in Pymol is there a way to align various NCS protein dsDNA > complex structure in asymmetric unit based on the double helix of DNA? > > I can do the align with the protein part with action-->align--> to molecule > or to selection. But this way does not work out if I select dsDNA and do > the align to selection. I also tried to used command align obj 01 and chain > X, obj 02 and chain Y to align dsDNA, but still failed with message > "invalid selection for alignment". > > thanks ahead for any input. -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A