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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