Hello, 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? Regards, Ali Algarrous
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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
Ali Algarrous wrote: > 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. Sure - that's exactly what model.transfer_xyz() will do. > 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? Absolutely, but that's a separate step, handled by a separate command - model.build(). If you look at the example script (examples/commands/transfer_xyz.py) you'll see that model.build() is called immediately after model.transfer_xyz() to do this. This will also build the coordinates for sidechains if the residue differs between target and template. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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