Hi Appu,

if I understand you correct then you have a structure with at least two 
domains. If you align two conformations of that structure, one domain 
does not get superposed nicely. Right?

The "psico" module provides the command "angle_between_domains", which 
is what you are looking for I guess.

Example: (tilted domain spans residues 100 to 150)

PyMOL> align s1, s2
PyMOL> select d1, s1 and resi 100-150
PyMOL> select d2, s2 and resi 100-150
PyMOL> angle_between_domains d1, d2

This requires "numpy" and "psico" installed.

Download psico:
https://github.com/speleo3/pymol-psico

Hope that helps.

Cheers,
   Thomas

Appu kumar wrote, On 11/01/12 04:50:
> Dear user
>                        Can you please help me in finding the angle
> between two structure upon alingment. I have aligned two structure and
> one structure is not perfectly aligned on other. There is domain of two
> structure tilting outward upon alignment. IS there any way to find the
> angle between two structure. Thanks in advances.

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