Ali Algarrous wrote:
I have a sequence and a structure aligned in a file in RIP format. Now I want to just copy the coordinates of our structure to our sequence without any changes. I am using transfer-xyz.py but it doesn't copy the coordinates as they are in the structure before or after the loops. Is there a way to transfer the coordinates from structure to sequence as they are?
transfer_xyz will copy coordinates of equivalent atoms in aligned residues, so if you want your model to have exactly the same coordinates as your template structure, you will need a 1:1 (gapless) alignment. If you have gaps/loops in your alignment, obviously Modeller will not be able to copy the coordinates since none exist.
What is it that you're trying to do?
Ben Webb, Modeller Caretaker
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