Re: Average structure

From: David Konerding <>
Date: Thu 29 Mar 2001 08:27:08 -0800

"Guanglei Cui" writes:
>I think MoilView by Carlos Simmerling and ptraj by Tom Cheatham both can
>generate average structures from dynamics. However, the averaged structure
>can be distorted, especially when there's large conformational change such
>as terminal base pair opening. I've seen the ring of one terminal base
>shrinked significantly. Minimization doesn't help to correct this as far as
>I know. Good luck!

Right, imagine the case of a sugar pucker which repuckers between C2' endo and
C3' endo. If the populations are 50% each, and you average them, you
end up with a planar sugar pucker which is physically impossible. Minimization
with pop the pucker down to the local minimum, but I doubt that's particularly relevant
or useful.

As for averaging, I usually use carnal or my own code. Once you've RMS aligned the
structures to a common structure, you can just do a vector additon of the coordinate
sets and then divide by scalar number of frames. Or, pre-divide and then sum.
Received on Thu Mar 29 2001 - 08:27:08 PST
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