Thanks for your reply, Eleanor.
The problem I had with LSQKAB is that it ONLY outputs the RMSD for the
residue range the superpose calculation based upon. What I wanted is to
superpose the two structures with the N-terminal 100 residues, but
calculate the RMSD for the entire structure (400 residues). Can LSQKAB do
that?
Best regards,
Huiying
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [email protected]
On Wed, 24 Nov 2010, Eleanor Dodson wrote:
Yes - I think there is a button on the GUI to click?
Eleanor
On 11/24/2010 01:58 AM, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ
Superpose in Coot by matching the first ~100 residues of the N-terminal
domain. Now I'd like to calculate the pair-wise RMSD for the entire
pre-superposed structures (~400 residues). Can LSQKAB output RMSTAB for
the two input PDB files without doing its own FIT/MATCH calculation?
Thanks,
Huiying
___
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [email protected]
