Actually I used compare.py as a means to narrow down the list with the 8 potential templates, not to generate an alignment for comparative modelling.
As for the consensus alignment (48 sequences and templates in total), it looks very good, all the conserved motifs from each sequence coincide. The problem is that sequence matches not necessarily imply structure matches, something that was denoted by malign3d when I fed the 8 template sequences as they were aligned in the consensus alignment.
Certainly my option 3 (letting Modeller align the sequences) is not a good idea as T-COFFEE's method is more sophisticated and incorporates structural information. So I'm between 1. and 2.
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 with only the selected 4 sequences and feed it to Modeller
Which of those 2 will be more accurate?
2010/2/4 Modeller Caretaker modeller-care@salilab.org
On 2/3/10 5:52 PM, Thomas Evangelidis wrote: > >> 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. >> > ... > > You don't have to use Modeller to generate your alignment - you can > generate it however you like (e.g. manually, with your favorite program, > etc.). There is also no requirement to align your templates with malign3d > (as you noted, that won't work unless the templates have a lot of structural > overlap anyway). So if you like your T-COFFEE alignment, by all means use > that directly (subject only to modifying the file format so that Modeller > can read it). > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >