VMD-L Mailing List

From: venkataraman kabaleeswaran (vkabs_at_yahoo.com)
Date: Tue Apr 12 2005 - 12:31:42 CDT

hi I am new to VMD.

I want to calculate the rotation angle between the two
different protein models, I did overlapping. I used
VMD
to calculate the rmsd, but it did not give the angle
of rotation between the two structures? can VMD can do
this calculation?

The overlapping is diffferent for different reference
point, example, if I use N-terminal as reference,
C-terminal moved quiet, if I used C-terminal as a
reference , then Central domain moved significantly.

Is any one know the correct way of doing overlap to
find out the rotation angle with respect to the
rotation axis?

What VMD can do in order to analysis two protein
structures?

thanks
cheers

Kabaleeswaran Venkataraman

Arise, Awake and stop not until goal is Reached
                           - Swami Vivekanand

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