[atomselect top "all"] set radius 2
set sel [atomselect top "name S"]
$sel set radius 1.9
#sphere scale 1 and radius 2 will make the particle's diameter 1 in the unit of box length
change particle number of color (atom type) with time steps in movie.xyz
put movie.xyz under the directory where tcl script access
topo readvarxyz movie.xyz
This will generate the needed xyz file and load it.
When specify atom name, add "and user > 0" as well # user > 0 are the original actual atoms
particles that are redundant are placed ad 0 0 0 and can be removed by adding 'user > 0'
to output this new xyz file do
topo readvarxyz movie_new.xyz selmod "all" # by default it's "user > 0"
which will have all color and atom changing features
color Name O red
how to only shown part of all particles?
index > 100 and index 150
how to draw rectangles?--just draw two triangles
draw triangle {x1 y1 z1} {x2 y2 z2} {x3 y3 z3}
in .xyz format, the atom name can be integer Z, which corresponds to element with atomic number Z
1 for H, 2 for He, etc...