[modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module

[Thomas Evangelidis <>]

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