VMD-L Mailing List

From: Andrew Dalke (adalke_at_mindspring.com)
Date: Tue Oct 30 2001 - 16:12:03 CST

Sanjeev B.S. <sanjeev_at_mbu.iisc.ernet.in>:
> Thanks a lot for the feedback. I was using the morph script
>available on the website and then I realized I need to superimpose. So I
>asked the question. I shall try to use superimposed cooridinates.

Did you also see the old VMDTech on morphing, at
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/0363.html
?

In contains a reference to the need for alignment
] Even though these two structures have the same topology (atom names,
] indicies, and residue names), they aren't aligned, so we'll need to
] apply an alignment matrix. For more information on this, see the
] previous VMDTech on "RMSD and best-fit alignments".

and that VMDTech is
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/0343.html

The trick is to realize the rms alignment code takes two atom
selections, and the atom selections can be told to use a specific
frame number. That second VMDTech contains an example of aligning
all the frames in an animation to the first frame.

Hopefully that works for your needs.

                    Andrew
                    dalke_at_dalkescientific.com