Cool Hunk wrote: > i have got an issue about the side chain of some of the aminoacids that > are part of some beta-strands in my predicted model.. is there any way > that i can rotate specific amino acids so that their side chains > orientation can flip outward which is inward in my predicted model... or > can i rotate the whole strand to fix that issue..

Once you've selected a set of atoms, you can rotate them about the origin or the mass center, or apply an arbitrary transformation matrix. See rotate_origin(), rotate_mass_center(), and transform() at http://salilab.org/modeller/9v7/manual/node214.html

> second question regarding some loops in my model is that one loop kind > of intersect the other or you can say passes in between/ thru the other > and that makes my model unreal.. can you tell me, how can i resolve this > issue????

Usually building multiple models and then selecting the best one with DOPE fixes this problem. The assessment methods are generally good enough to detect knotted models like this.

Ben Webb, Modeller Caretaker