Re: [modeller_usage] Help with transfer_xyz method

[Ali Algarrous <>]

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 <>
Sent Sat 6/30/2007 9:10 PM
To Ali Algarrous <>
Cc 
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
-- 
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