On 09/03/2018 06:23 AM, Marko Sever wrote: > The biggest problem I'm seeing is that helices > strands and loops which dont have a template structure to align to > (since the similairty is 60% and the identity is 30%) are just floating > in space, they are not in a "natural" position. How do I fix that first?
If you don't have a template, Modeller isn't going to know where to put them. It will do its best to enforce proper stereochemistry, but yes, I would expect them to be floating in space. You would need additional input information, such as distance restraints, to pin them down.
> Secondly maybe it even is accepting the secondary structure restraint, > but it is severly beding the helices, since it wants to aggresivly align > to the template structure...with which parameters would I handle this so > I could get a reasonable structure?
Modeller will always make your model follow the template - that's how it works. If you don't want to align part of the structure to the template, alter the alignment so that those residues are aligned to gaps instead.
Ben Webb, Modeller Caretaker