[Chimera-users] Rainbow by secondary structural element?

Tom Goddard goddard at sonic.net
Wed Jun 25 10:04:08 PDT 2014


Hi Oliver,

  I added a “rainbow helix” command to Chimera, in tonight’s daily build.  Unfortunately it doesn’t look much different then simply using rainbow when applied to a transmembrane protein.  The two image below show "rainbow helix” and “rainbow” on 2rh1.

      

They are different since the rainbow helix command does not color the turns  and beta strands, and it has constant color on each helix, but those differences are hardly noticable.  I also discovered that the rainbow command only applies to whole models.  So it colors all helices even if you specify only the transmembrane residue range, so “rainbow helix :29-230,263-342” gives the same coloring as “rainbow helix”.

	Tom


On Jun 25, 2014, at 8:01 AM, Oliver Clarke wrote:

> Hi all,
> 
> Currently, the rainbow function can operate at the levels of per residue, per chain or per model.
> 
> I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element?
> 
> This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). 
> 
> Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary.
> 
> Cheers,
> Oliver.
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> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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