want to select all atoms instead of only Calpha atoms

[Ayesha kanwal]

in this code only all C-alpha atoms for trajectory frame superposition are selected ca.inds <- atom.select(pdb, elety="CA") but i want to select all atoms also for trajectory frame then how can i select it please guide me.

[Lars Skjærven]

Hi Ayesha, atom.select allows you to select the atoms you want. you can use various input arguments to this function. e.g. atom.select(pdb, "noh") will select all non-hydrogen atoms in your PDB. Use help(atom.select) for a more complete overview of your options here.

Below is an example where I superimpose to the backbone atoms. Note that this assumes that your pdb and trajectory file contains the same number (and order) of atoms.

# select backbone
sele <- atom.select(pdb, "backbone")

# access backbone coordinates 
# trj[1, sele$xyz]

# fit trajectory coordinates
xyz <- fit.xyz(fixed = trj[1, ], mobile = trj, fixed.inds = sele$xyz, mobile.inds = sele$xyz)

Hope this helps.

[Ayesha kanwal]

ok i got it thank you so much