[gmx-users] DSSP=> how to edit .eps file

[David van der Spoel]

On 2010-04-04 06.40, Chih-Ying Lin wrote:
>
> HI
>
> 1. dssp -n index.ndx
> => only atom numbers of one residue in the index.ndx
> => can dssp decide the exact second structure for the only one residue
> without considering other residues of protein?
no.


> => can i get the same second structure for the residue with [ dssp -n
> one-residue.ndx ] and  [dssp -n protein-main chain + H .ndx ] ?
no.

>
>
> 2. The legend indicates the color of different second structure is shown
> under the secondary-structure plot.
>      I don't want to change the colors assigned, but one legend is
> half-shown. The picture of legend is cut.
>     How can I get that legend full-shown.
>
send your command lines.
>
>
> 3. With the option
> -sss         string  HE
>
> HE = helix ?
no, this is DSSP coding. H = helix , E = extended (Beta sheet), B = beta 
turn, T = som other kind of turn, 3 = 3-10 heix, 5 = pi helix.
>
>
> Thanks
> Lin
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se