>1) Do you recommend any specific manufacturer? Why?
For molecular biology, protein structure, and performance, it
is difficult to do better than Silicon Graphics. They run GCG and
other software packages and are the standard for 3D-structure
visualization. They currently are competitively priced and memory and
peripherals are available from 3rd party vendors. SUN does not have
anything that compares (at the price), IBM is trying but does not have
the software, and DEC's Alpha may be there in a year or so but they
are also playing catch-up in the software department.
Buy 50 MHz R4000 workstations. Equip some with appropriate
graphics engines and leave the rest to do slower graphics or other
computations. I would stay away from the higher-priced multiprocessor
machines; the workstations are far more cost effective.
I think SunOS is a much nicer unix in some ways (lpd), but
even Sun has given up on it, so go with Silicon Graphics.