Re: [Jmol-users] Need definitions of protein, nucleic

[Timothy D. <mol...@ma...>]

On Jan 5, 2006, at 1:46 p, Eric Martz wrote:

> For a revision I am making to firstglance.jmol.org, I need  
> definitions of the predefined atom sets "protein", "dna", "rna",  
> and "nucleic". By that I mean I need the lists of group names for  
> amino acids and nucleotides that are selected when you "select  
> (protein,nucleic)". Can someone please give me those lists from the  
> Jmol source code?
>
hi Eric,

see the file src/org/jmol/viewer/JmolConstants.java, especially  
starting around line 1675, for details.

protein and nucleic are determined by atomic composition, not by  
group names.  if I remember the rules correctly, any group with N,  
CA, and C is part of the protein set.  (amino is still determined by  
group names, though - ala, arg, asn, etc.).  the carbonyl O can be  
either O or O1, and I can't recall if that is required for inclusion  
in the protein set.  I don't think so.

for nucleic acids, any group that has the backbone sugar atoms (O5',  
C5', C4', C3', O3', C2', C1') is part of the nucleic set.  the  
presence of an O2' distinguishes RNA from DNA.

hope that helps,

tim
-- 
Timothy Driscoll                                em: mol...@ma...
molvisions - see. grasp. learn.                 ph: 919-368-2667
<http://www.molvisions.com/>                    im: molvisions
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