Re: [modeller_usage] doutbs about file

[Modeller Caretaker <>]

Amanda Moraes wrote:
> My name is Amanda Maia and I´m a beginner using Modeller. I´m having 
> some trouble finding the answers to my questions on the manual. Could 
> you help me?
> I have a sequence that aligns (BLAST pdb)with various structures on PDB 
> within an average identity of 35%. Since I need to use as much models as 
> I can get, I´m writing a PIR file with 5 templates. But one (1MDY) has 2 
> chains (out of 4) that blast quotes (B and E). Do I have to make a PIR 
> line to each one? And a pdb file for each one too?
>  
> Example:
>  >P1;molde1MDYB
> structureX:molde1MDYB:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00
> ----------------------------------------------------------------------------------------------------------------------------TTNADRRKAATMR--ERRR------LSKVNEAFETLKRSTSSNPN-----------QRLPKVEILR--------NAIRYIEGLQAL-LRD-------------------------------------*
>  
>  >P1;molde1MDYA
> structureX:molde1MDYA:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00
> ----------------------------------------------------------------------------------------------------------------------MELKRKTTNADRRKAATMR--ERRR------LSKVNEAFETLKRSTSSNPN-----------QRLPKVEILR--------NAIRYIEGLQAL-LRD-------------------------------------*

Sure, you will need a sequence in your alignment file for each template. 
But you can use the same PDB file for the two chains - you can just tell 
Modeller in the sequence headers which chains to read out of the PDB, 
for example:

>P1;tmplB
structureX:foo:FIRST:B:LAST :B::: 2.00:-1.00
-----*

>P1;tmplE
structureX:foo:FIRST:E:LAST :E::: 2.00:-1.00
-----*

This would use two templates, called 'tmplB' and 'tmplE', each of which 
is a single chain read from the PDB file 'foo.pdb'. You could also use 
real residue numbers rather than 'FIRST' and 'LAST' if you wanted to 
read only part of each chain. See 
http://salilab.org/modeller/9v4/manual/node438.html for more information.

	Ben Webb, Modeller Caretaker
--
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