Thank you so much for your response. This is also what I was expecting that transfer_xyz is not going to do what I want.
Let's say I have something like this:
>P1;1a1t structureX:1a1t:FIRST:A:LAST:A:::: MQKGNFRNQRKTVKCFNCGK---EGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN---*
>P1;madeup sequence:madeup:::::::: MGKGNFRMQRKTVKCFNCGKD--EGHIAKNCRMNCDKGCWKCGKEGHQMKDCTERQANGRT*
I want Modeller to copy the coordinates of the template to my sequence for at least (N CA C CB) atoms of each residue. And if there is a gap/loop, then Modeller should generate the coordinates for it.
Is there anyway that Modeller would do what I want?
Thank you in advance.
Regards, Ali Algarrous
-----Original Message----- >From Modeller Caretaker modeller-care@salilab.org Sent Sat 6/30/2007 9:10 PM To Ali Algarrous algarra@uni.edu Cc modeller_usage@salilab.org Subject Re: [modeller_usage] Help with transfer_xyz method
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