Measuring Angles is another matter, but the superposition services of
the DrugSite will align an arbitrary selection of DNA residues (the
moving molecule) onto a target residue selection on another
structure. The selection can include a duplex, or even a duplex and
some protein residues.
LSQMAN aligns just about anything, incl. DNA and RNA -
http://xray.bmc.uu.se/usf/lsqman_man.html
There's a ready-to-use macro that will do all the hard work for you -
ftp://xray.bmc.uu.se/pub/gerard/omac/align_rna.lsqmac - there's one line that
may need editing, it defines the name of the nomi
orted by lsq. But it
is more common to look at DNA geometry directly for changes (3DNA or Curves+).
Original message
From: "Veerendra Kumar (Dr)"
Date: 04/12/2013 2:18 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA structures superimpose
Dear C
The concept of a "domain" in a DNA structure is a bit obscure. Could you be
more explicit about what you are trying to do? Do you mean protein domains in a
protein-DNA complex?
James
On Apr 12, 2013, at 12:18 AM, Veerendra Kumar (Dr) wrote:
> Dear CCP4 members,
> Is there any program to supe
Dear CCP4 members,
Is there any program to superimpose the DNA structures? I also want to measure
the relative domain rotation angle. I tried using DynDom but it does not work
for me.
Can someone suggest a program which can output the rotation angles?
Thank you
Best Regards
Veerendra kumar
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