how to merge more than two groups ?
I want to analysis my dna-ligand using bio3d.
a.inds <- atom.select(pdb, resid="CYT")
b.inds <- atom.select(pdb, resid="GUA")
c.inds <- atom.select(pdb, resid="THY")
d.inds <- atom.select(pdb, resid="ADE"),I want to merge all this.
sele <- combine.select(a.inds, b.inds, c.inds, d.inds operator="OR") using this command I got error Error: unexpected symbol in "sele <- combine.select(a.inds, b.inds, c.inds, d.inds operator"
I tried to select two groups,
sele1 <- combine.select(c.inds, d.inds, operator="OR")
sele1 <- combine.select(c.inds, d.inds, operator="OR") it is ok but I want to combine four groups,so How can I merge them ?
Could you guide me please ?
Comments (3)
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reporter -
reporter I have another question.I want to calculate my ligand rmsd.
lig.inds <- atom.select(pdb, resid="UNK")
lig.xyz <- xyz[, lig.inds$xyz]
rd <- rmsd(xyz[1,lig.inds$xyz], xyz[,lig.inds$xyz])
plot(rd, typ="l", ylab="RMSD", xlab="Frame No.")
points(lowess(rd), typ="l", col="red", lty=2, lwd=2)
so I did.But I want to calculate my ligand noh ,
lig.inds <- atom.select(pdb, resid="B noh")
lig.xyz <- xyz[, lig.inds$xyz]
rd <- rmsd(xyz[1,lig.inds$xyz], xyz[,lig.inds$xyz])
Error in apply((apply(b[, b.inds], 1, "-", a[a.inds])^2), 2, sum) :
dim(X) must have a positive lengthso How can I could ?
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check your command
lig.inds <- atom.select(pdb, resid="B noh")
. Is the double quoted a valid residue ID? “noh” should be a value given to the argumentstring
.
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