CCP4's superpose does this.
It produces a table like this, but only for residues that are used in
the alignment.
.-------------.------------.-------------.
| Query | Dist.(A) | Target |
|-------------+------------+-------------|
| + A:ARG 10 | |H+ A:GLN 223 |
| + A:ARG 11 | |H+ A:ASN 224 |
|H+ A:LYS 12 | <..6.19..> |H+ A:PRO 225 |
|H+ A:LYS 13 | <--4.03--> |H+ A:ASN 226 |
|H+ A:LYS 14 | <--3.73--> |H+ A:GLN 227 |
|H+ A:GLN 15 | <..4.05..> |H- A:LEU 228 |
|H+ A:LYS 16 | <..3.41..> |H- A:ILE 229 |
|H+ A:GLU 17 | <..1.75..> |H. A:SER 230 |
|H- A:ILE 18 | <++1.97++> |H- A:LEU 231 |
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
On 11/28/2011 02:53 PM, Jacob Keller wrote:
Let me refine my question (sorry for my lack of clarity): is there a
program that will output the distances between the corresponding ca's
of a superposition on a residue-by-residue basis, and not just a
global RMSD value (doubtless these numbers are part of the
superposition algorithm itself)? I want to plot these values as a
function of residue number to show which parts of the structures
deviate more or less from each other.
Jacob
