There's a typo there:
"none", "turn", "sheet", "helix", "dna", "rna", "carbohydrate",
"helix310", "helixalpha", or "helixpi"
that's 0-9.
On Fri, Mar 1, 2013 at 10:22 AM, Rolf Huehne <[email protected]> wrote:
> Hi all,
>
> Q: How must the numbers returned by the atom property function
> "{selected_atom}.substructure" be translated into the corresponding
> secondary structure types?
>
> The scripting documentation (13.0 and 13.2) contains this description:
> ------------
> Used with select substructure=x, x can be either the quoted keyword
> "none", "turn", "sheet", "helixalpha", "dna", "rna", "carbohydrate",
> "helix310", or "helixpi", or the respective number 0-9. In the context
> {*}.substructure, the return value is a number; in the context label
> %[substructure], the return is one of the nine keywords. (Jmol 12.0)
> ------------
>
> In Jmol 13.1.13 in the example '1DEH, chain A, residue 47' the number
> returned (=8) does not correspond to the position of the keyword
> 'helixalpha' (=4 if counted from 1; =3 if counted from 0) which is
> reported by the label command.
>
> For the for example residues below only three would fit into the keyword
> list from the documentation (0,2,7; if counted from 0):
>
> 111.CA = 0 = none
> 7.CA = 2 = sheet
> 361.CA = 7 = helix310
> 47.CA = 8 = helixalpha
>
> Besides there are mentioned 10 numbers (0-9) but only nine keywords.
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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