On 3/5/10 1:51 AM, Ajeeta kaushiki wrote: > I have to generate a hetero dimer . The entire length of protein is > 1500 amino acid . The first dimer is from 150-410 aa and next one is > from 786-1188 aa , I have modelled this two domains separately , Now I > have to map it on a known Homo Dimer present in the template pdb to > generate as a heterodimer . Kindly guide or is there any other way to > merge the coordinates .
Modeling of a heterodimer is straightforward - you do not have to do anything special. It's just regular modeling, in this case with two templates, and with a chain break in your sequence if you so desire. See also FAQ #1: http://salilab.org/modeller/FAQ.html#1
By the way, your question suggests that you have no template for the following regions: 1-149aa, 411-785aa, 1189-1500aa. These insertions are far too large for Modeller to model reasonably (15aa is about the limit for loop modeling). Thus, you would be better off building a model for only the aligned regions.
Ben Webb, Modeller Caretaker