Re: [modeller_usage] optimization protocol and HETATM flexibility

[Modeller Caretaker <>]

On 11/20/12 6:32 AM, sdimicco wrote:
> class dope_loopmodel(dope_loopmodel):

While this *might* work, it'll be confusing to people reading your 
script. Normally, you would use a different name for your derived class, 
e.g.

class MyModel(dope_loopmodel):
...

a = MyModel(...)


> a.make()
>
> automodel.final_malign3d = True

This last line will have no effect, since you set the flag after you 
call make(). If you want to do a final malign3d, do

a.final_malign3d = True
a.make()

> Moreover, I built a model with an HETATM residue. If I want to treat it
> as flexible residue: how could I do that?

You'd have to make a new residue type (or get the parameters from an 
existing source) and use the new one letter code in the alignment. See
http://salilab.org/modeller/9.11/FAQ.html#8

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage