Re: [modeller_usage] modeller 9.2: spaghetti effect with multiple templates

[Modeller Caretaker <>]

Raik Gruenberg wrote:
> already a while ago I have noticed that modeller tends to produce what I 
> would call spaghetti proteins (containing knots and other fancy 
> structures) when it is supplied with multiple templates that are far 
> from the target (35 % or less) and also quite diverse among each other.
>
> However, Modeller 9 seems to suffer more from this effect than the 
> previous versions

Just to resolve this for the benefit of the modeller_usage list: a bug 
in Modeller 9v1 caused the original template structures to be used in 
the generation of its initial model. This is different from the Modeller 
8 behavior, in which the templates were first modified by 
alignment.check() (which does all pairwise superpositions). The Modeller 
8 behavior has been restored in the new Modeller release, 9v2.

	Ben Webb, Modeller Caretaker
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