SSM - see superpose task under Coordinate utilities.
This matches secondary structure and gives RMSD for CAs - inceredibly
useful program..
Eleanor
On 11/19/2010 10:55 PM, Srivastava, Dhiraj (MU-Student) wrote:
Hi All
does anyone know any software that can calculate and print out RMSD
On 22:55 Fri 19 Nov , Srivastava, Dhiraj (MU-Student) wrote:
> does anyone know any software that can calculate and print out RMSD of
> every residue (c alpha will be good) for homologous structures which
> has only 30-40 % sequence similarity? I looked on the web but all the
> software that
On Nov 19, 2010, at 4:00 PM, Srivastava, Dhiraj wrote:
Hi All
does anyone know any software that can calculate and print out
RMSD of every residue (c alpha will be good) for homologous
structures which has only 30-40 % sequence similarity? I looked on
the web but all the software tha
Dear Dhiraj;
Please try the following web site
http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html
Here you will find a number of option for structure base sequence
alignment no matter what is the similarity of your structures. Regarding
the RMSD of every residues you can find this option
>I looked on the web but all the software that I found require the sequence
to be the same for both structure.
most modern programs perform some kind of local-global alignment first
to define the corresponding residues and then compute the statistics.
BR
On Friday, November 19, 2010 02:55:54 pm Srivastava, Dhiraj (MU-Student) wrote:
> Hi All
>does anyone know any software that can calculate and print out RMSD of
> every residue (c alpha will be good) for homologous structures which has only
> 30-40 % sequence similarity? I looked on the w
Hi All
does anyone know any software that can calculate and print out RMSD of
every residue (c alpha will be good) for homologous structures which has only
30-40 % sequence similarity? I looked on the web but all the software that I
found require the sequence to be the same for both struc
