Both pymol/align and coot/ssm (I presume) do the secondary structure alignment first followed by structural alignment. So it only works for proteins. In Pymol, there is "fit" command that instead matches atoms with the same names; and "super" which does sequence alignment first. You can try to play with those instead. And of course, coot has the LSQ option where you can specify which residues/nucleotides you would like to match. Some of these options (or all) will do the trick.
On Wed, 2009-10-21 at 11:06 -0400, Mike England wrote: > Hi all, > > I will highly appreciate your help regarding following: > > How to align two DNA structures in Pymol or Coot or any other softwares? > ( I tried regular "align" in Pymol, but it doesn't work for DNA; it > works great for protein structures.) > > > Thanks a lot in advance ! > > > Mike --
