Distance matrix using center of mass

[Former user]

I was wandering whether it is possible to output a matrix of distance (dm) using the center of mass of the residues and ligands in a protein?

Many thanks in advance,

Alexander

[Xinqiu Yao]

Hi,

Yes, it is doable, but you need to write a simple script to do it. For example,

pdb <- read.pdb('1tag')

# remove water
pdb <- atom.select(pdb, 'water', inverse=TRUE, value=TRUE)

# Get all atom masses and split them according to residues
m <- atom2mass(pdb$atom[, 'elety'])
id_res <- paste(pdb$atom[, 'chain'], pdb$atom[, 'resno'], pdb$atom[, 'insert'], sep='_')
mass <- split(m, id_res)

# Split xyz according to residues
xyz <- split(pdb$xyz, rep(id_res, each=3))

# Calculate center of mass of residues
com <- as.numeric(sapply(unique(id_res), function(i) com.xyz(xyz[[i]], mass=mass[[i]])))

# distance matrix
dm <- dm.xyz(com)

plot.dmat(dm)

Let me know if you have any question!