Re: To Model missing domains in the content of the rest
Dear MODELLER experts,
I have a target protein, whose X-ray structure is PARTIALLY available (the middle part, named domain B). There are two big regions missing (domain A & C) in the crystal structure, with more than 50 residues in each I would like to use MODELLER to model domain A & C, and there are templates available. I wonder if it is possible to include THE CONTENT OF domain B. in another word, to create a complete model of A-B-C while keep the coordinates of B domain fixed.
Any help/information will be greatly appreciated.
Shirley
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Shirley Li wrote: > I have a target protein, whose X-ray structure is PARTIALLY available > (the middle part, named domain B). There are two big regions missing > (domain A & C) in the crystal structure, with more than 50 residues in > each I would like to use MODELLER to model domain A & C, and there are > templates available. I wonder if it is possible to include THE CONTENT > OF domain B. in another word, to create a complete model of A-B-C while > keep the coordinates of B domain fixed.
Of course - just use the B domain structure as a template for that part of the sequence, and your other templates for the rest of the sequence. If you really don't want it to move at all, just unselect that domain: http://salilab.org/modeller/manual/node28.html
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Shirley Li