restrict salign to subparts of some structures sequences
Hello modellers,
I have a very large dataset of (beta propeller domain) structures, which I inspected visually to assess parts that sounded obviously not relevant for a structural alignment. For some structures I spotted long loops or several small helices insertions which I would like salign not to consider during the structural alignment. Is there a way to do so ?
thanks
--Ben.S
On 04/18/2011 02:14 AM, Benjamin SCHWARZ wrote: > I have a very large dataset of (beta propeller domain) structures, > which I inspected visually to assess parts that sounded obviously not > relevant for a structural alignment. For some structures I spotted > long loops or several small helices insertions which I would like > salign not to consider during the structural alignment. Is there a > way to do so ?
No, not with SALIGN. The only way to do that that I can think of would be to feed it structures with those regions removed, then add them back in afterwards. But if you already have an alignment you're happy with, superpose() can certainly ignore these regions - simply exclude them from the selection.
Ben Webb, Modeller Caretaker
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Benjamin SCHWARZ -
Modeller Caretaker