Deep View (SWiss PDB viewer) isn't available for linux anymore, and the old versions rely on 32 bit libs (which is increasingly a headache on debian). Rasmol is a classic, but I haven't used it properly since 1997 -- and all attempts at exporting png, jpg etc. failed on my debian wheezy box.
Jmol is awesome, and while I managed to make some pretty convincing figures I never quite got to where I wanted.
So I tried pymol
Pymol, like rasmol and jmol, has a visual interface which can be controlled via an integrated terminal. The learning curve is steep, but it's quick and easy to make figures once you've got the basics.
Install pymol from the repos in debian:
sudo apt-get install pymol
(on Archlinux you can get it via AUR -- you'll need to install python-pmw first)
Download 1SU4.pdb from here http://www.rcsb.org/pdb/explore.do?structureId=1su4
In the directory where your pdb file is, do
pymol 1SU4.pdb
Click on the A(ction) by (helices), select preset/publication.
show spheres, calcium
Note that 'helices' and 'calcium' are just handles or aliases that I made up.
alter calcium, vdw=5
show spheres, calcium
color purple calcium
bg_color white
set antialias=1
set sphere_mode=5
where sphere_mode 5 means shading.
ray 1000,1000
save 1SU4.png
And here's the final figure:
