On 2/11/10 6:04 AM, Heidi Tuominen wrote: > I am doing model of homodimeric protein. I have two parts and from > both of them I have template structure. Between them there is linker > which is based on homologous proteins and 2D prediction helix. I want to > my model that helix and symmetric homodimer.
You can certainly create a helix restraint in Modeller, but first and foremost Modeller builds models that look like the templates. If your linker template is not a helix, chances are the linker will look like that template rather than any helix restraint you try to enforce.
> 1) If I do first model with helix and then symmetric homodimeric > model - I loose helix. > 2) If I do first symmetric model and them restraint helix - I loose > a bit symmetry.
Do you mean you build a model and then use that model as the template for a second modeling run?
> Is it possible to do these to restraints in one run?
Yes, certainly.
> My .py file (#? - marks for helix in previous run)
Your script looks fine, except that you are adding the helix restraints in user_after_single_model(). That function is called after the model building is finished, so those restraints won't have any effect. Move that into the special_restraints() function instead.
Ben Webb, Modeller Caretaker