Hi, I want to graft the loop from some other protein taken from pdb to my protein structure. I tried modeling it on my own but some parts of the secondary structure (beta sheet) also change into loop while loop modeling .. So I want to fix those two ends of the beta sheet where the loop is present so that these end should not change to loop region. Is it possible using modeller and if it's possible .. is it logically correct as during my modeling study I found that some part of beta sheets get converted to loop .. so fixing the ends of beta sheet while loop modeling would be sensible or not ?? Pls guide ----------------- Bharat
On 1/24/11 12:01 AM, bharat lal wrote: > I want to graft the loop from some other protein taken from pdb to my > protein structure.
You could use multiple-template modeling to achieve this. Alternatively, you could manually combine the two PDB files, using a PDB viewer or even by editing the files in a text editor.
> I tried modeling it on my own but some parts of the > secondary structure (beta sheet) also change into loop while loop > modeling ..
That is hardly surprising - loop modeling does not use any information from the template.
> So I want to fix those two ends of the beta sheet where the > loop is present so that these end should not change to loop region.
If you don't want to subject the beta sheet to loop modeling, simply don't select those residues in the select_loop_atoms function: http://salilab.org/modeller/9v8/manual/node34.html
Ben Webb, Modeller Caretaker
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