Straight-off I'd go for the higher sequence id. But yes - much better to use both. Choice needs to consider what your model is for. Also what are the other features of these templates, e.g. are they complexed with anything? You should take a look at the TvLDH example using MODELLER, which would appear to be very relevant to your question. It makes an excellent tutorial - demonstrating how the first template choice whilst having a significantly beter seq. id. than other alternatives did not in the long run turn out to be so useful as there was poor resolution in the active site region. So this was then combined with another template, having better resolution in that region, though poorer overal seq. id, and the combo produced a far better final model.
Mike
-----Original Message----- From: Alex Brown [mailto:abrown@nimr.mrc.ac.uk] Sent: 04 October 2002 15:22 To: modeller_usage@salilab.org Subject: Basic Modeling Question
Hi. Sorry if this question seems a bit basic, but you don't learn if you don't ask, and you may as well ask the experts.
The alignment of the target sequence with a suitable template is, perhaps, the most important factor in producing a good model. However, choosing a suitable template can be a problem. There appear to be two factors :
1) Sequence identity; and 2) Template resolution.
Which is more important ? For example, I have a couple of possible templates I could use :
Template A : 87% identity, 2.80Å resolution Template B : 62% identity, 1.60Å resolution.
Would it be better to use both ?
Cheers,
Alex.