On 02/09/2010 08:57 AM, nornik wrote: > When I used salign with several templates I noticed that the *fit_fit* > files have new coordinates. Sure, because it sounds like you asked SALIGN to perform a structural alignment. > I assumed that MODELLER tried to place them > in the same coordinate system according to the sequence alignment > produced by salign to get "better" starting positions before energy > minimization. No - the comparative modeling procedure does not use SALIGN (or any other structural alignment) by default. > I have compared the different *fit* "clusters" and, to me, it seems like > the first fit sort of places the main (top) template in some sort of > origo and the following fits (*fit_fit*, *fit_fit_fit*) align the other > templates with the main one according to the sequence alignment produced > by salign. Yes, this will be the behavior if you set the SALIGN option fit_on_first to True. > Due to these observations I assumed that you had to transpose the > template pdb files so that they were sort of placed "correctly" with > respect to eachother. No, that only affects the generation of the initial structure. > "If no additional information is available about the relative > orientation of the two domains the resulting model will probably have an > incorrect relative orientation of the two domains when the overlap > between A and B is non-existing or short. To obtain satisfactory > relative orientation of modeled domains in such cases, orient the two > template structures appropriately before the modeling." Yes, this will give a better initial model. But if there is no overlap, there will be no restraints between the domains, so they will move around. > But with sufficient overlaps you think I can just use the original > template pdb files and disregard the fit steps performed by salign? Yes, that should be fine. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage