My observation is that the aligned frames were away from the reference by
both translation and some type of rotations - it does not seem to be a
simple translation between the reference and the aligned frames.
Wen
On Fri, 1 Apr 2005, Thomas E. Cheatham, III wrote:
>
> > In addition to my previous message, I randomly chose a frame from a
> > trajectory, and add this frame to the beginning of the trajectory which I
> > want to align to the added first. The result is that the trajectory is not
>
> Are you sure that the frames are not aligned? (i.e. even though they are
> not at the same location in space, they are relatively aligned?) If not,
> this is a problem; if they are simply translated, this is the expected
> behavior (as implemented). I think the earlier ptraj versions (and maybe
> even the current) translate the center of mass of the reference
> coordinates to the origin (to simplify things). If this centering is
> implicitly occuring (which my quick read of the code suggests), you can
> overcome this by finding the center of mass (of the atom selection) for
> your reference coordinates and manually translate (using the translate
> command) after fitting... Alternatively, you can center .P of the
> reference coordinates to the origin (in a separate ptraj run).
>
> Otherwise, the rms() routine in rms.c would have to be modified to shift
> the transformed coordinates back to the center of mass of the reference
> coordinates. I have to think a bit more about (and test) the implications
> of such a change, but I think it may actually be the right thing to do
> here (i.e the rms code should not implicitly center to the origin but to
> the center of mass of the reference coordinates) and should be a
> relatively simple code change...
>
> --tom
>
>
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Received on Fri Apr 01 2005 - 22:53:00 PST
