New FREE PDB Viewer for Macintosh

Manuel C. Peitsch mcp13936 at ggr.co.uk
Wed Jan 24 07:15:58 EST 1996

Hi everybody!

A new tool named Swiss-PdbViewer is available on the WWW



Swiss-PdbViewer is a Macintosh application that can display
PDB files. Several proteins can be analyzed at the same time
and can be "piled-up" in 3D space by picking 3 corresponding
reference atoms of the structures to align. RMS differences
can then be calculated on selected amino acids of the aligned
proteins using alpha carbon atoms, backbone atoms, sidechain
atoms or all atoms. The comparison of active sites and other
relevant regions is therefore very easy. Swiss-PdbViewer can
also measure distances, angles, torsions angles between atoms
as well as add/remove amino acids to/from the view with simple
mouse clicks thanks to the intuitive graphic and menu driven
interface. A Control Panel regroups all of the most frequently
used display facilities so that display/undisplay of individual
amino acids sidechain, van der Waals dots surface, color, atom 
types and names (according to [1]), are accessible with a single 
click. H-bonds can be estimated for the whole molecule even if the 
PDB file does not provide explicit H atoms, and it is possible to 
mutate amino acids sidechains by browsing a rotamer library [2]. 
The best rotamer is automatically suggested.
Furthermore, during the mutation process, H-bonds and steric
hindrances are automatically estimated and displayed in real
time, facilitating the best rotamer choice. Views can be
exported as Pdb files, Picts files, or Pov [3] scenes
descriptions. The short-term purpose is to develop a
multi-platform (MAC, PC, UNIX) modeling package that will
allow multiple sequence alignements as well as directly 
submit modeling requests to the SWISS-model server [4].

[1]	Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., 
	Ghio, C., Alagona, G., Profeta, S.,Weiner, P.K. (1984) 
[2]	Ponder, J.W. et al. (1987) J.Mol.Biol. 215:403-410
[3]	Pov is a popular multi-platform free Ray-tracer that
	can be retrieved by anonymous FTP from: 
[4]	Peitsch, M. C. Bio/Technology 13:658-660.

Nicolas Guex and Manuel Peitsch
Glaxo Institute for Molecular Biology
ch. des Aulx 14,
1228 Plan-les-Outes/Geneva  

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