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
Hi Mike,
By 'align', if you mean superimposition, lsqman will do the job.
Raji
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Raji Edayathumangalam
Joint Research Fellow
Brigham and Women's Hospital/
Harvard Medical School
Brandeis University
On Oct 21, 2009, at 11:06 AM, Mike England wrote:
Hi all,
I will highly
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
Anna Pyle's group came out with a powerful idea- a simplified set of
torsion angles for nucleic acids (NA).
http://nar.oxfordjournals.org/content/vol31/issue16/images/small/gkg682f1.gif
http://nar.oxfordjournals.org/cgi/content/abstract/31/16/4755
This is implemented in a Perl program, called
