On Wed, 24 Mar 2004 11:56:16 +0000 Binbin Liu bmbbl@bmb.leeds.ac.uk wrote:
> Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance.
Modeller calculates each structure by an algorithm that uses random numbers to search for the best positions for each part of the molecule. This means that each structure will differ slightly, even though the same data (the templates) were used as input to the algorithm. This is why you see the variation - its not really by chance though. There are energy functions involved in side-chain placement, and a final optimisation stage that moves them around so they don't touch too much.
Side chain torsion angles are actually quite difficult to get right - they are the 'fine detail' of structure, and making them perfect means having a highly accurate model of the system. There are tools dedicated to modelling side-chains efficiently - search for SCWRL by Roland Dunbrack at the fox chase CRC, for one example. Even then, if the model of the backbone is not perfect, then the side-chains are not likely to be 100% correct.
j. _______________________________________________________________________ Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics Hamburg http://www.zbh.uni-hamburg.de/staff.php