[gmx-users] minimum distance matrix and secondary structure

David spoel at xray.bmc.uu.se
Thu Nov 13 21:48:01 CET 2003

On Thu, 2003-11-13 at 20:56, Q.Z. wrote:
> Dear All,
>  I heard that the average minimum distance matrix can be used to 
> identify secondary and tertiary structure and then can be used to 
> monitor the changes of these structural elements with time.
>  Now I have used g_mdmat to generate the NxN matrix. How do I visually 
> identify the these structures on the contour map, in terms of the 
> location of alpha-helix, beta-sheet, etc? Thanks.
helices show up as a pattern of n,n+4 dark spots
sheet as off-diagonal lines, either parallel to the diagonal or
perpendicular to it

> Q. Zou, PhD
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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