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