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Re: [modeller_usage] Help with transfer_xyz method

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
--
             http://www.salilab.org/modeller/
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