VMD

To load a pdb:

vmd> mol load pdb filename.pdb

To add trajectories:
vmd> mol addfile filename type ccd

Select residues (p.69 VMD manual)

In the menu 'graphics'-'representations' select the molecule and 'create rep' to create a new object; then to select specific residues write in the box "selected atoms"

all resid xxx

to select specific atoms in a residue and represent it in a different style:

name ~HD2 and resid 124

then select i.e. CPK fot this new representation (this would show CPK for atom HD2 only belonging to residue 124). 
To select residues within 7A from atom HD2 on residue 124:

within 7 of name ~HD2 and resid 124

How to smoothen trajectory

1. source traj_smooth.tcl (make sure the file is in the path where VMD started)
2. set sel [atomselect top "all"]
3. set avgpos [avg_position $sel avg.pdb beg 0 end last writesel selonly] (this writes out the pdbfile with average position)