[Jmol-developers] Re: color by structure for DNA/RNA

[Miguel <mi...@jm...>]

>>I am starting to work on the graphic shapes for nucleotide chains.
>>Backbone and Trace are partially working.
>>
> cool.

They are starting to look pretty good :-)

>>The color scheme 'structure' defines colors for
>>helix/sheet/turn/random segments of amino acid polymers. We can say:
>>
>>load samples/pdb/1crn.pdb
>>trace on
>>color trace structure
>>
>>However, if we try this on 1D66, we see that the DNA strands are
>>colored white ... the same as random turns.
>>
> yes, that is Chime/Rasmol compatible behavior.
>
>
>>It seems to me that this color scheme should be extended to provide
>>special colors for DNA and RNA.
>>
> a good idea, but somewhat more difficult...
>
>
>>
>>Q: Should we use the Dark Purple and Maroon colors that you defined
>>for DNA & RNA as part of the DRuMS color scheme?
>>
> the DRuMS schemes do not color nucleic acids by structure, only by
> identity.

Good point.

> I don't know how to determine the structure of nucleic acids,
> analagous to the DSSP algorthims for defining protein secondary
> structure.
>
> maybe such an algorithm exists - can anyone else comment on this?

How about this ... If it is DNA or RNA then we color by identity, not by
structure?

I have implemented it and checked it in. Take a look and let me know what
you think.


Miguel