[modeller_usage] modelling fragments

[Viktor Hornak <>]

Dear All,

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.
If some Modeller expert could provide advice or point out what I am 
doing wrong, I would greatly appreciate it...

Thanks!
-Viktor

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Viktor Hornak
SUNY at Stony Brook
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