Re: [modeller_usage] modelling fragments

[Modeller Caretaker <>]

Viktor Hornak wrote:
> I was trying to use Modeller to produce coordinates of parts of a given 
> target sequence based on full PDB coordinates of a template.
> For example: my template has a sequence  AAAAABBCCCCCDDEEEEE which 
> represents three helices (AAAAA, CCCCC, EEEEE) connected by two loops 
> (BB, DD). My target has a sequence aaaaabbcccccddeeeee (again three 
> helices and two loops) and I would like to overlap target helices on the 
> template helices such that the loops in target are ignored. In other 
> words, the resulting coordinates for the target would just have three 
> helices (aaaaa, ccccc, eeeee). I have tried different alignment 
> variants, such as:
>
>  >P1;mol1
> structureX:mol1:1: :19: : :2.2:
> AAAAABBCCCCCDDEEEEE*
>
>  >P1;mol2
> sequence:mol2: : : : : : :
> aaaaa--ccccc--eeeee*
>
>
> but the target sequence always wants to be connected; I don't know how 
> to make Modeller to produce three helical fragments modeled on template 
> helices of the full PDB structure.

The sequence is connected because Modeller builds CHARMM stereochemical 
restraints on all atoms in a given chain, which include inter-residue 
backbone restraints. To get multiple fragments, just break the chain at 
the appropriate places by putting in chain break characters ('/'). So 
your alignment might look like

>P1;mol1
structureX:mol1:1: :19: : :2.2:
AAAAABBCCCCCDDEEEEE*

>P1;mol2
sequence:mol2: : : : : : :
aaaaa/-ccccc/-eeeee*

	Ben Webb, Modeller Caretaker
--
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