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How does one color superimposed stuctures?

Andrew Dalke dalke at ks.uiuc.edu
Fri Jun 7 15:37:52 EST 1996

> I have several structures I would like to superimpose and graphically
> display with a ribbon backbone. [...] I would like to blend the colors
> of the superimposed backbones,

  I can tell you how to do it with our molecular graphics program,
VMD (http://www.ks.uiuc.edu/Research/vmd/), and I imagine the same
trick can be done in other programs as well.

  Basically, combine the two structure in one file, making sure the 
coordinates don't overlap (otherwise the bond connection algorithm
will be messed up).  You should also give each structure a different
chain or segment identifier so you can distinguish between them (eg,
A and B).

  Read the combined file, then fit B to A.  Draw one ribbon as "segname
A and not within 1 of segname B", another as "segname B and not within
1 of segname A", and the third as "(segname B within 1 of segname A) or
(segname A within 1 of segname B)".  Color each of the selections the
way you want.

  I just did it using two structures picked at random from the Protein
Motions data base (http://hyper.stanford.edu/~mbg/ProtMotDB/); two
structure of lactate dehydrogenase, which are PDB accession numbers
6LDH and 1LDM.  It wasn't hard, just tedious, but then, I'm one
of the authors of VMD.  Email me direct if you want more info.

						dalke at ks.uiuc.edu

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