Molecular Graphics on PCs

Mahmut Miski miski at KODAKI.KODAK.COM
Wed Jul 22 09:08:59 EST 1992


I use "Alchemy III" and "PCModel, v. 4.0" on my Mac. In addition to
its native format, Alchemy (from Tripos Associates, Inc.) can read
and write MM2, Sybyl formats but only able to read PDB and X-ray
crystallographic data. Alchemy offers real-time animation during
wire-frame display mode, also able to display space filling (CPK),
cylinder and ball-stick models in both mono and stereoscopic form. The  
graphical output (to screen and printer) of Alchemy is superior to the
PCModel. However, molecular dynamic calculations (energy minimization) of
PCModel appears to be more reliable than Alchemy. K. Gilbert's PCModel can
read and write MM2, Macromodel, MOPAC, X-ray crystallographic data, Sybyl,
Chem-3D and PCM formats. Both packages are commercial, however, they offer
substantial discounts to the academic users.

I believe these packages might handle small to mid-size molecules properly,
however, for proper handling of large molecules (i.e., proteins) one might 
need faster machines (Mac Quadra line or 486 DOS Machines) as well as a lot 
of RAM's on the board. Nevertheless, even under these conditions performance
of these programs will not be close to those high end molecular graphics
packages running on workstations with a dedicated high resolution monitor.  

M. Miski                                      Miski at kodak.com
Sterling Winthrop Pharmaceuticals R & D




More information about the Bio-soft mailing list