Dear Modellers,
I have a protein domain with very low sequence identity to PDB structures
(37%), therefore I created a nice consensus alignment with T-COFFEE which
includes both sequences and templates. After carefully inspecting the
alignment, discarding bad matches, and realigning, I ended up with 8
potential templates which all look good to me. Thus I tried to adapt the
compare.py script used in the basic tutorial, to help me select the best
templates. Initially I tried to feed my consensus alignment instead of
aligning the templates with aln.malign() command, but that failed when
executing aln.malign3d() because the overlap between the template sequences
is very small (I got an error about the number of equivalent positions being
insufficient). So I eventually aligned the template with aln.align() and
selected 3 of them for comparative modelling.
Now, after that observation, I 'm a bit confused. Should I :
1. edit my T-COFFEE-generated consensus alignment by leaving only the 4
sequences I need, and create an alignment for Modeller
2. generate a new structure-based alignment with T-COFFE including only the
selected 4 sequences and feed it to Modeller
3. use alignment() module to align the 4 sequences
Which is the best option? Any suggestion will be greatly appreciated.
Tom