Troy Wymore wrote:
>
> Hello MODELLERs,
>
> I am new to MODELLER and would like to know if there is an easy way to
> accomplish this task. I have a raw sequence that I want to align with my
> 3D structural alignment that contains nine sequences.
> First, it seems like my raw sequence should be formatted so that MODELLER
> can read it. Since this is just a sequence with no corresponding structure
> shouldn't the second line of the sequence file just be:
>
> sequence:
>
> It seems strange to me that in the manual all the examples of sequences
> have a corresponding PDB code when the point of homology modelling is to
> create the model hence no PDB code. Or for this do I just make one up?
Sure, you can.
>
> If the sequence file for the target is then correct can I do the
> following:
So far I do not see any objections to that, as long as the gaps in
seq...ali are
make sense in the context of the str...ali
The only thing I don't understand is that why would you need to do that,
when both
structures and sequence can happily live in one alignment for the
MODELER purposes?
(Advantage of keeping them in one file is to be able to see easily the
quality of str-seq
alignment in any editor with fixed size fonts)...
My two cents,
Azat.
>
> READ_ALIGNMENT FILE = 'structures3d.ali', ALIGN_CODES = 'all' # my 3D
> # structural alignment for nine structures
>
> SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES
>
> READ_ALIGNMENT FILE = 'sequence.ali', ALIGN_CODES = 'all' # my target
> # sequence
>
> SET OVERHANG = 0
> ALIGN2D GAP_PENALTIES_1D= -400 -150, GAP_PENALTIES_2D = 0.5 0.5 0.5 0.5
> 0.5 6
>
--
- Azat Badretdinov, Ph.D.
- Molecular Simulations Inc.
- 9685 Scranton Road
- San Diego CA 92121-3752
- Phone: (858) 799 5728