Re: [modeller_usage] Combining steps in Basic and Advanced Tutorial ?
To: Ashika Umanga Umagiliya <>
Subject: Re: [modeller_usage] Combining steps in Basic and Advanced Tutorial ?
From: Modeller Caretaker <>
Date: Wed, 04 Mar 2009 12:34:25 -0800
Ashika Umanga Umagiliya wrote:
> I follow the steps 1 and 2 in the 'Basic tutorial'.
> Then using the generated 'build_profile.prf' during step 2; I select
> upto maximum 5 templates with lowest e-value.
> Then I proceed with steps on 'Advanced tutorial'.ie in 'salign.py', I
> use above selected templates for modelling..
> How accurate is my procedure?
The accuracy will depend on the sequence identity and the quality of
your alignment, but your approach is probably reasonable. Of course, if
your templates all have very low sequence identity to the target, it is
unlikely that the generated model will be accurate. Secondly, if the
templates are also very similar to each other, the structural alignment
of them all is likely to be a good one - if not, you may need to remove
one or more templates, or adjust alignment parameters.
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage