Dear Xiao Lei, You can try the command given below to align structures. Before you do that you have to create mobile and target chains to different objects.
align mobile, targeted, transform=0/1; transform=0(without) / 1(with superposition) For more options refer the pymol wiki (https://pymolwiki.org/index.php/Align ) Best regards, Thiru On Mon, May 15, 2017 at 10:34 PM, Stefan Gajewski <sgajew...@gmail.com> wrote: > Dear Xiao Lei, > > You might want to consider UCSF Chimera for this task > > https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ > matchalign/matchalign.html > > Best, > Stefan >
