Re: [modeller_usage] How to discard overhangs in target sequence

[Oliver Hucke <>]

Hi Markus,

you might modify your alignment like this:

>P2;template
-----------------YYYYYYYY------------------
>P1;target
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

should become

>P2;template
-----------------YYYYYYYY------------------
>P1;target
-----------------XXXXXXXX------------------

i.e. you might simply delete all parts from the target sequence that you 
do not want to be modelled.

Hope this helps,
Oliver



Markus Fischer wrote:
> Hello modellers,
>
> if my target sequence is longer compared to the template sequence and in 
> the alignment I find an overhang for the target sequence at the N- and 
> C-terminus, is there any way to tell modeller by some parameters to use 
> only the part of the target sequence covered by the template, or do I 
> have to cut the overhang in the alignment?
>
> Thanks,
>
> Markus.


--
_______________________________________

Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific St
Seattle, WA 98195
T:(206)685-7046
_______________________________________