Respected Sir, First of all, congratulations for the MODELLER's 9.11 release.
I have a small query. For a considered well reliable template, is it possible that i can also use the side chain information exactly the same way from the template, i.e. MODELLER uses the complete backbone and side-chain information for the aligned residues from the considered template, and accordingly the MODELLER then predicts the left over residues through the earlier considered reliable scaffolds? Please guide me the same way.
Sincerely, Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
On 9/8/12 9:59 AM, Ashish Runthala wrote: > I have a small query. For a considered well reliable template, is it > possible that i can also use the side chain information exactly the > same way from the template, i.e. MODELLER uses the complete backbone > and side-chain information for the aligned residues from the > considered template, and accordingly the MODELLER then predicts the > left over residues through the earlier considered reliable > scaffolds? Please guide me the same way.
You can simply select only the "left over" residues for refinement: http://salilab.org/modeller/9.11/manual/node23.html
Ben Webb, Modeller Caretaker
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Ashish Runthala -
Modeller Caretaker