On 11/02/2012 11:41 AM, Mehdi Talebzadeh Farooji wrote:
I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated.
It is certainly possible to introduce suitable distance restraints by overriding the special_restraints() method in automodel (you might also find it necessary to add some angle restraints to get the coordination right). But note that if your model is aligned with the template in this region, Modeller will add its own restraints, which might conflict with yours. You may need to modify the alignment (e.g. so that the model is not aligned with the template) or override the nonstd_restraints() method:
http://salilab.org/modeller/9.11/manual/node70.html
Ben Webb, Modeller Caretaker
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