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Re: [modeller_usage] to model only specific region

On 5/18/10 3:02 AM, Nicee wrote:

I have a pdb file(pdb1.pdb) which is having some missing residues like from 89
to 96 and 137 to 141,etc. I wish to model only this missing region such that
rest of the structure remains the same as in the initial pdb(pdb1.pdb). I have
searched a template(pdb2.pdb) having 64% identity with sequence(seq1)of pdb1. Is
it possible to model the missing residues using pdb2 as template but the
remaining portion of pdb1 remains the same.
Yes, this is possible. Just make an alignment between your sequence and two templates - align pdb2 with your sequence in the missing regions, and pdb1 in the other regions.
If you don't want the pdb1 parts of your sequence to move at all, only select the pdb2 parts for refinement. See 
http://salilab.org/modeller/9v8/manual/node23.html

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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