subscript out of bounds

[imren bayil]

Hi,I want to calculate ligand rmsd,

lig.inds <- atom.select(pdb, "ligand")

lig.xyz <- xyz[, lig.inds$xyz]
Error in xyz[, lig.inds$xyz] : subscript out of bounds
rd <- rmsd(xyz[1,lig.inds$xyz], xyz[,lig.inds$xyz])
Error in xyz[1, lig.inds$xyz] : subscript out of bounds I am getting this error,How to fix it ?

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[Xinqiu Yao]

Can you prepare a short example for us to check?