DSSP plotting vs residues number

[Former user]

is it possible to plot DSSP result (residue number wise) i can analyze trajectory with dssp, but i could not find any function to plot the secondary structure contents

[Xinqiu Yao]

Hi,

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You can use the R primitive function image to do it. Below is what I did:

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Suppose you have a matrix named ssmat, which contains the time series of secondary structure for all residues (row represents time and column residue number). Secondary structures are represented as 0 (helix), 1 (sheet), and 2 (other). Then,

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image(x=1:nrow(ssmat), y=0:ncol(ssmat), z=ssmat, zlim=c(0,3), col=c(“red”, “green”, “blue”, “white”), xlab=”Frame No.”, ylab=”Residue No.”)

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