[MMTK] protein setup

Asbjorn Christensen asbjorn@fysik.dtu.dk
Thu, 15 May 2003 16:05:22 +0200


Dear MMTK users,

is there any simple way to initialize the position of atoms
in a protein directly from a given letter sequence ["Ala", "Gly", "Tyr", ...]
WITHOUT reading an experimental PDB file (of the entire protein)?

Of course, this be done in a variety of not non-sense ways, e.g. a
"linear" chain. If anybody has a simple example of translating
a letter sequence to a sensible all-atom protein model (with positions defined),
this will be appriciated.

PS:  is Examples/protein_construction.py in the online dokumentation 
       up to date? Our MMTK installation has 
       highest "last revision:" ==  2002-6-3

Best wishes, Asbjorn
-- 
Asbjorn Christensen, PhD
CAMP, Physics Department, Building 307
Technical University of Denmark, 
DK-2800 Lyngby, Denmark
   
E-mail:       asbjorn@fysik.dtu.dk
Telephone: (+45) 45 25 32 27
Telefax:      (+45) 45 93 23 99
office:         room 257