Re: [modeller_usage] umber of equivalent positions < 3

29 Nov 2010


      On 11/25/2010 05:21 AM, bharat lakhani wrote:
>                           I am getting this error, when i am running
> modeller. i posted this mail before but i did not get any reply.
...
> _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3:
>      1
Looks like you are trying to do a structural alignment of two proteins 
that are not aligned in sequence, e.g. your input alignment looks 
something like:
protein1    AAAAAAAA--------*
protein2    -------BBBBBBBBB*
protein3    CCCCCCCCCCCCCCCC*
There is no way that Modeller will be able to structurally align 
protein1 with protein2, because it needs at least 3 equivalent positions 
to do that (there is only one above).
Ben Webb, Modeller Caretaker
-- 
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