How to specify whole protein structure in trajectory analysis?

[Former user]

Hi All, The bio3d tutorial for trajectory analysis has explained the method to superimpose Ca atoms only by this command [ca.inds <- atom.select(pdb, elety="CA")], but I want to select the whole protein structure means including the side chains as well. Can you please help me how to do this?

Thanks in advance!

Amir

[Xinqiu Yao]

You can select protein by atom.select(pdb, 'protein') or non-hydrogen atoms atom.select(pdb, 'noh'). Check help(atom.select) for more detail.