Deleting the loop /unessential regions is a more robust way to go. You will be surprise to see that how much those regions can contribute the clashes. Increasing clash tolerance in Phaser makes the program runs really slow and gives ambiguous results.
Best, Nian On Wed, Oct 21, 2009 at 11:41 PM, Vandana Kukshal <v_kuks...@cdri.res.in> wrote: > hello > > > > i have 3.25 A data of multidomain protein with 4 individual domain .one > domains structure is already known . and for others domain 40 % simmilar > structure is known . when i am running phaser with one known domain i am > getting the solution but after getting solution i am serching other domains > but clashes are coming . > > how should i proceed . > > > > thanx > > > > >
