how to merge more than two groups ?

[imren bayil]

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 ?

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[imren bayil]

sel1 <- atom.select(pdb, resid="ADE")
sel2 <- atom.select(pdb, resid="THY")
sel3 <- atom.select(pdb, resid="GUA")
sel4 <- atom.select(pdb, resid="CYT")
sel <- combine.select(sel1, sel2, sel3, sel4, operator="+")
Union of selects

• Selected a total of: 2003 atoms *
• I did ! Thank you

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[imren bayil]

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 length

so How can I could ?

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[Xinqiu Yao]

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 argument string.

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