How define restrains between model and template?
Hi,
The bend of the modeled three strands long sheet differs too much from the template. Independently that perhaps that have meaning. I want to make closer to the template. It is not clear (or I am missing it ) if is possible restrains between model and template.
Thanks in advance
Mario
On 3/28/18 8:35 AM, Mario A Bianchet wrote: > It is not clear (or I am missing it ) if is possible restrains between > model and template.
It isn't necessary to define restraints to the template, since Modeller does that automatically. If your model is deviating from the template, then you either have a lack of restraint in that region (generally due to a poor alignment, such as a gap) or you have some sort of restraint conflict (e.g. multiple conflicting templates, or steric clash).
Ben Webb, Modeller Caretaker
Dear Ben Webb
Thanks for your answer. Looking to the alignment and model, the region have low identity but the alignment is sound. I am not see any evident/obvious problem with alignment or steric clashes. Let me rephrase the question: it is possible to increase the weight of such restrains on a particular region ?
Mario
On 3/28/18 6:14 PM, Modeller Caretaker wrote: > > On 3/28/18 8:35 AM, Mario A Bianchet wrote: >> It is not clear (or I am missing it ) if is possible restrains >> between model and template. > > It isn't necessary to define restraints to the template, since > Modeller does that automatically. If your model is deviating from the > template, then you either have a lack of restraint in that region > (generally due to a poor alignment, such as a gap) or you have some > sort of restraint conflict (e.g. multiple conflicting templates, or > steric clash). > > Ben Webb, Modeller Caretaker
On 3/29/18 11:05 AM, Mario A Bianchet wrote: > Let me rephrase the question: it is > possible to increase the weight of such restrains on a particular region ?
Sure, you can tweak the weights by adjusting schedule_scale; see https://salilab.org/modeller/9.19/manual/node19.html
Ben Webb, Modeller Caretaker
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Modeller Caretaker