Re: [modeller_usage] a question about add hidrogen

[Modeller Caretaker <>]

Atila Iamarino wrote:
> I have this py file to include disulfide bonds:

Looks good to me.

> I want to include hidrogens to the protein

That's straightforward - just subclass the allhmodel class rather than 
automodel, i.e. replace the line
class mymodel(automodel):
with
class mymodel(allhmodel):

You should be aware that including hydrogens will result in your models 
taking roughly 4 times as long to build (since you have roughly twice as 
many atoms).

> and a substrate that's on one 
> of the templates

Just add relevant BLK residues ("." characters) to your alignment, and 
turn on env.io.hetatm. See the examples in the manual and tutorial.

> And by the way, 
> modeller does not make simmulated annealing wrigth?

I'm not sure what you mean. If you mean, "does Modeller do simulated 
annealing?" then yes, it does. The standard model building procedure 
combines conjugate gradients minimization with molecular dynamics 
simulated annealing refinement.

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