Re: [modeller_usage] Symmetry and helix

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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