[gmx-users] DSSP=> how to edit .eps file
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 4 08:58:48 CEST 2010
On 2010-04-04 06.40, Chih-Ying Lin wrote:
> 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?
> => can i get the same second structure for the residue with [ dssp -n
> one-residue.ndx ] and [dssp -n protein-main chain + H .ndx ] ?
> 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.
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
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