Try this:
T1 = readtable('Fe3O4_1.txt');
x = T1.Var4;
y = T1.Var5;
z = T1.Var6;
[AtomLbl,ID] = findgroups(T1.Var2);
FeLbl = (AtomLbl == 1);
OLbl = (AtomLbl == 2);
figure
Feh = scatter3(x(FeLbl), y(FeLbl), z(FeLbl), AtomLbl(FeLbl)*20, AtomLbl(FeLbl), 'filled');
hold on
Oh = scatter3(x(OLbl), y(OLbl), z(OLbl), AtomLbl(OLbl)*30, AtomLbl(OLbl), 'filled');
hold off
grid on
axis('equal')
colormap([1 0 0; 0 1 0])
legend([Feh, Oh], ID)
xlabel('x')
ylabel('y')
zlabel('z')
producing:
.
