[Chimera-users] morphs

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 17 15:06:51 PDT 2014


Hello Moses,
It is not necessary to have the same number of atoms (or residues), the method takes care of that.  You can even morph between different but related proteins as long as their sequences are similar enough to align easily.

However, the models *must* have the same number of chains.  You can still display the "extra" chain(s) by simply opening an additional copy of the structure that has more chains.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing>

More specifically, in the case you mentioned:
(1) open structure of enzyme
(2) open structure of enzyme+DNA as another model, but delete the DNA part so that these first two models will have the same number of chains
(3) use those first two models for morphing
(4) open another copy of the structure of enzyme+DNA, use to display DNA (can hide or delete the rest)

You can script making the DNA appear at a specific frame in playback of the morph trajectory or fade in gradually (see MD Movie per-frame scripting or "coordset","transparency" commands).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
<http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html#transp>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 16, 2014, at 11:15 PM, Moses Adenaike wrote:

> Hello Chimera users,
>  Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA.
> Moses




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